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The Designs of Biological Forms, Development, and Initiation of Cancer

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Contents

INTRODUCTION...............................................................................................................................................................................1PRIMORDIALIZATION..........................................................................................................................................................................5Emergence of biological forms requires primordialization: changing of an urprimordial cell into a primordial cell..........................................................................5Forms' designs are encoded by the invariant proteins during the process of primordialization...............................................................................................6Forms cannot be transformed................................................................................................................................................................8HOW PRIMORDIALIZATION WORKS TODAY?.........................................................................................................................................................11Sources of cells equivalent to urprimordial cells..........................................................................................................................................11Egg cells are replicates of primordial cells...............................................................................................................................................16Functions in multicellular organisms derive from cell's functions in urprimordial cells....................................................................................................16PROTEIN INTELLIGENCE.......................................................................................................................................................................19Protein molecules have the ability to recognize events and memorize their sequence.........................................................................................................19Protein molecules can program and reprogram the events inside the cell.....................................................................................................................20DNA IS PASSIVE AND CHANGEABLE..............................................................................................................................................................25DNA has a passive role in cell affairs.....................................................................................................................................................25DNA plays a passive role during development................................................................................................................................................26DNA has no role during cell division.......................................................................................................................................................27DNA mutations and organisms' designs.......................................................................................................................................................28The high content of non-functional DNA in multicellular organisms is possibly the result of dumping non-coding DNA sequences...............................................................30DEVELOPMENT................................................................................................................................................................................33Reasons for the similarities of organs during embryonic development between different organisms according to Darwin's theory of evolution and primordialization theory.....................33INITIATION OF CANCER.......................................................................................................................................................................41Destabilization of a cell's primordial program leads to initiation of cancer...............................................................................................................41Distinction between the process that leads to the formation of Placenta and the process that leads to initiation of cancer.................................................................43ADAPTABILITY ENSURES THE SURVIVAL OF LIVING ORGANISMS AS DISTINCT FORMS....................................................................................................................45Adaptability helps living organisms to survive, and preserve their identities..............................................................................................................45Adaptability is not dictated by the environment............................................................................................................................................47SEXUAL REPRODUCTION........................................................................................................................................................................51The design of sexual organs cannot be achieved by random mutations.........................................................................................................................51Sex differentiation........................................................................................................................................................................53The purpose of sexual reproduction.........................................................................................................................................................54BEHAVIOUR..................................................................................................................................................................................57Relation between survival strategies of unicellular organisms and behavior in metazoan.....................................................................................................57Some examples of instinctive behavior showing foresight....................................................................................................................................60Instincts and competence for survival at birth.............................................................................................................................................61Humans have been learning the means of survival from animals...............................................................................................................................62BIODIVERSITY...............................................................................................................................................................................65Darwin-Wallace's arguments on biodiversity.................................................................................................................................................65Biodiversity as viewed by primordialization theory.........................................................................................................................................67Similarity of sequence between homologous proteins and estimates of the rate of DNA mutations provide no evidenceof phylogenetic relationships.............................................69'Form' versus 'species'....................................................................................................................................................................73Fossil finds and the problems associated with them.........................................................................................................................................76SUMMARY OF THE THEORY......................................................................................................................................................................89CONCLUSION.................................................................................................................................................................................91REFERENCES.................................................................................................................................................................................99

Chapter One

Emergence of biological forms requires primordialization: changing of an urprimordial cell into a primordial cell

For the emergence of any kind of biological form an urprimordial cell, a design, and a design-making program is required. I call this design-making program 'primordial program'. A primordial program has to be integrated into an urprimordial cell and turn it into a 'primordial cell'. The process of changing an urprimordial cell into a primordial cell I name 'primordialization'. A primordial cell can then develop into a form, and the program it contains determines the design of that form, as it has been explained below.

Urprimordial cells are the very first living cells that emerged on earth. They must have been able to grow and reproduce; otherwise, they would have died out soon after they emerged. They would have also ceased to exist, if they were not been able to communicate with the environment surrounding them. In order to accomplish this, those cells must have been equipped with signalling proteins on their surface that could establish such communication, crucial in their search for nutrients. In addition to the qualities mentioned above, cells derived from a dividing urprimordial cell must have possessed the potential to remain, under favourable conditions, attached to each other. Further, the pores on the surface of the derived cells must have been able to join end to end and establish intracellular channels. Those were the two prerequisites for the urprimordial cells to turn into multicellular organisms, later.

Forms' designs are encoded by the invariant proteins during the process of primordialization

What kinds of molecules are encoding primordial programs? The answer to this question is this: Primordial programs are being encoded by some of the invariant proteins that are present in urprimordial cells. I consider the following invariant proteins as the very likely candidates among them to take part in encoding the primordial programs: proteins such as those that determine the polarity of organisms; proteins in charge of segmentation and symmetries in developing embryos; growth factors; growth factors receptors; proteins that are involved in signal transmission; and proteins that are in control of DNA molecules. The number of the invariant proteins that are being used for making primordial programs constitutes only a fraction of the urprimordial cells' proteins, but they can encode theoretically thousands of different primordial programs depending on their number, their location The Designs of Biological Forms, Development, and Initiation of Cancer inside or on the surface of the cells, and their manner of interaction with each other. In other words, primordial programs differ from each other by the way those invariant proteins are combined and arranged during the primordialization processes. In this way a primordial cell obtains the information for the ultimate appearance, function, and behaviour of the organism to which it develops. The information on the design of a multicellular organism present in its primordial cell needs to be translated into a comprehensive plan that has to be read after each cell division throughout the entire processes of development and differentiation. In other words, each cell in a developing embryo has to be provided with a set of instructions defining its specific duties. How this takes place? At any level of development and cell differentiation the organism's primordial program (alternatively, I refer to it as design regulative program) adjusts the activities of the subordinate regulative proteins. With this the design regulative program makes sure that the cells' activities remain within the boundary of the organism's general design. While the job of the design regulative program is to code the design of the form and preset its boundary, the functions of the subordinate regulative proteins are to lead the cells and organs to develop within that preset boundary. Passing of information in this manner will continue from one cell generation to the other until the structure of the organism is complete.

Forms cannot be transformed

According to primordialization theory no biological form can be transformed into another. When any of the proteins involved in the primordial program of a cell is altered, genetically or epigenetically, this would have disastrous consequences for that cell or even for the organism as a whole, because those proteins cannot tolerate alterations. In case such an alteration takes place in a primordial cell, or an egg cell as its replicate, that cell would either die or give rise to nonviable deformed structures. When alteration of a protein involved in a primordial program occurs in a somatic cell, that cell would turn into a cancer cell. I will talk about this under the heading 'Initiation of cancer' later. Here, I want to emphasis that I prefer not to use the term transformation to describe the turning of a normal cell into a cancer cell, because I apply this term strictly with regard to the designs of organisms. Instead, I call such changes aberrations; to this I also include any changes that distort the general features and proper functioning of a biological form. For example, an anencephaly that is caused by a defect in a subordinate regulative system responsible for the formation of head structures is an aberration in vertebrates and invertebrates alike, because none of those animals when born with anencephaly is representing a new form; with or without head they are the same organisms. Very different from this kind of anencephaly is the anencephaly in chelicerates, which is not an aberration, because their primordial cells are so programmed that these animals have no heads, and that the organs which are operating in head section in other arthropods are located in their prosoma section [the bodies of chelicerates are subdivided into two sections, the prosoma (front) and the opisthosoma (back). The prosoma contains segments that bear the chelicerae (spider's fangs), pedipalps and four pairs of walking legs. It carries the main feeding, sensory, and locomotor apparatus].

How primordialization works today?

It works as reprimordialization using cells equivalent to urprimordial cells.

Sources of cells equivalent to urprimordial cells

As it has been mentioned above, the process of primordialization needs urprimordial cells. However, since free-living original urprimordial cells are unlikely to be available on earth any more, cells equivalent to them are being used in this process. Such cells can be produced when, for example, an organism or parts of it disintegrate into undifferentiated cells through disintegration of its original primordial program. However, these cells only then can take part in primordialization process when the amino acid sequences of the proteins involved in their original primordial program are not changed. Then, the proteins from the original program are reprogrammed into a new primordial program. I call this reprogramming process 'reprimordialization'. In the following I describe some sources of cells equivalent to urprimordial cells together with examples of reprimordialization.

1. Some embryonic cells in placentals can be turned into cells equivalent to urprimordial cells. The external cells of their embryos at 8-16-cell stage (the merula) are such cells. Some of them develop into a trophoblast leading to the formation of placenta. I consider these cells equivalent to urprimordial cells for the following reason. Placenta, I believe, is an organism, not an organ. If it were an organ, then it must be integrated into the anatomy of the organism that continues to grow after the birth. Furthermore, the fact that it nourishes inside the uterus independently from the foetus underlines this notion. Reprimordialization requires that the external merula cells in order to be able to lead to the formation of placenta, first of all, their original primordial program must be erased. This means that they become equivalent to urprimordial cells. These cells are then reprogrammed getting a new primordial program, which determines the design of the placenta. It needs to be mentioned that this process should not be mixed with the ability of embryonic cells in some organisms to reproduce offspring, such as the larvae of Trematoda. In this case no primordialization process is required, because the daughter embryos and the embryo that gives rise to them have the same design and so the same primordial program.

2. Cells equivalent to urprimordial cells can be produced trough partial or total disintegration of some metazoan organism under a process that has been called, incorrectly, metamorphosis. Let me explain this by taking Drosophila as an example. An egg laid by Drosophila fly grows into a Drosophila larva, which is a form with a design totally different from the fly form. The fly, contrary to the current notion, is not the product of further development of the larva, because it has its own distinct design. The design of the fly seems to be programmed inside a group of cells that in the literature are being referred to as imaginal cells [A fertilized egg begins its development with a series of very rapid nuclear divisions with no cell division. Most of those nuclei migrate from the middle of the egg toward the surface, where they form a syncytium. Later plasma membranes grow inward from the egg surface to enclose each nucleus, converting the syncytium into a blastoderm consisting of some 5000 separate cells. Thereafter, the larva emerges and passes through three stages, or instars, separated by molts in which it sheds its old coat and cuticle and lays down a larger one. When the life of larva nears the end, its tissues break up. Its disintegrated epidermis cells are deposited in different segments of that organism (imaginal discs). The organs of the fly develop from this group of cells]. Interestingly, those cells are undifferentiated. I assume that during the disintegration process the larva cells are being cleared from their original primordial program and reverted to undifferentiated cells. Since they have the original proteins still active for reprogramming, they are equivalent to urprimordial cells. As such they can be reprimordialized. This means that they can acquire through rearrangement of those proteins a new primordial program specific for the design of the fly form of the Drosophila. I predict also the existence of a reprimordialization process for the emergance of the larva form of the Drosophila. This possibly takes place at an early stage of the oogenesis in the fly.

3. The production of urprimordial cells is also very obvious by nauplius larvas of parasitic copepod Haemocera danae, when they become parasite in a polychaete worm. Inside the host the life of nauplius larva reaches an end; its structures disintegrate, leaving no sign of a larva behind. What is left after this disintegration is an ovoid mass of small undifferentiated cells. This mass of small undifferentiated cells is equivalent to urprimordial cells. These cells then give rise to a new form, a free-swimming organism inside the worm. Here, a reprogramming of the first primordial program into a new one takes place, i.e. a reprimordialization.

In this place I want to substantiate my notion that larvae, no matter to which taxonomic group they belong, are distinct biological forms. They are active, feed themselves, and with some exceptions they live independently. In addition, larvae and the 'adult' organisms can live under very different environmental conditions. A larva can live parasitic, while the 'adult' organism lives free (e.g., Gordioidea), or the larva can live free, while the 'adult' organism is a parasite (e.g., parasitic copepods). Finally, many larvas instead of turning into the so-called adult organisms, can reproduce independently, either asexually (e.g., Cecidomya), or sexually (Cetenophora). It is noteworthy that Darwin himself founded undisputable that larva and 'adult' organism during metamorphosis represent two independent organisms, when he wrote, "No one probably will dispute that the butterfly is higher than the caterpillar."

4. Cells equivalent to urprimordial cells are produced as part of the process that leads to the emergence of medusas from a hydroid polyp. They are produced through disintegration of parts of the polyp. The polyp usually produces its own kind, i.e. other polyps, through budding. Occasionally, some of those buds behave differently and produce medusas. To do this they have to disintegrate and form gametangia. It is during this process that the polyp's primordial program is being replaced by a primordial program specific for the design of the medusa. Thus, the cells inside the gametangia are equivalent to urprimordial cells, in order for the reprogramming to take place.

5. I consider processes such as the one that turns the unicellular amoeba Dictyostelium discoideum into a multicellular slug also reprimordialization. When facing starvation, the amoebae assemble into multicellular mounts. The cells within the aggregates then turn into undifferentiated cells. These cells reorganize themselves and lead to the formation of a multicellular organism, the slug. For this to happen the undifferentiated cells have to be cleared from the primordial program of the amoeba (become equivalent to urprimordial cells) and subsequently be furnished with a new primordial program, one which determines the design of the multicellular slug. This example could possibly reflect the situation when the original urprimordial cells started to aggregate to give rise to the first multicellular organisms on earth.

Egg cells are replicates of primordial cells

Since in Metazoa the regulative program concerned with the basic design of organisms and the strategies of their subsequent development rest inside their egg cells, these cells must obtain those proteins that are essential for the designs of their respective forms always in the same composition and sequence in order to get the green light for starting the development process. For this reason I consider egg cells as replicates of primordial cells. I find a number of findings in the literature that are in agreement with this notion. In mouse zygote it has been found that the first cleavage occurs 17-20 hr. after fertilization, and no mRNA synthesis occurs during this period. In Drosophila, the proteins that determine the initial polarity and the spatial coordinates of the developing embryo are already present inside their unfertilized eggs [It has been demonstrated that egg cells in which any of those proteins are altered produce embryos that fail to survive for lacking large parts of their bodies such as head, thoracic, and abdominal sections].

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