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There are two types of genes, the kind that code for the synthesis of some specific protein, and the kind that help to determine when that protein synthesis will be done. Proteins, in turn, catalyze all the chemical reactions from which the intricate biochemistry of a living organism is constructed. That is how it all happens. It is all driven by chemistry. The question is why the off-springs are like there parent life form and not different. Exception is a mutation in genes. After fertilization Zygote is formed. Then it go on dividing by mitosis to produce ball of cells called as Morula. Then cavity is formed inside and you have outer cell mass and inner cell mass. Inner cells are going to form the organism. Then you have two layers of cells. 1) Ectoderm 2) Endoderm. Now fate is sealed. Once you go forward you can not go back. From the ectoderm cells you can get tissue derived from ectoderm only. From the endodermal cells, you get tissue derived from the endoderm only. Then cells from ectoderm enter inside to form mesoderm. Mesoderm cells can form tissue of mesoderm only. With formation of Pro-chordal plate head and tell end is fixed. Ectoderm invades inside the mesoderm to form the neural tube and crest. Now fate is sealed. It is going to form the nervous system. True for every system but you take brief example of nervous system. 100 billion cells and some of them will form cerebrum, some cerebellum, some thalamus, some hypothalamus, some caudate nucleus, some put-amen, some globes Pallid-us, some corpus callosum, some corpus stria-tum, Some limbic system, ,Some medulla oblongata and Spinal cord. At each step information is transferred in most coordinated manner and each cell acts accordingly. So permutations and combinations of about 20,000 to 25000 cells is enough to dictate 100 Trillion cells minus 25 trillion red blood cells. You have Each body cell has 'same' genetic coding and there are so many types of cells having many Anatomical structures and Physiological functions. So each type of cell work under leadership of particular gene and others perform the functions of assistance at different category. Here is no Ego. Intention is to get job done. And genes do it. How they do it, is beyond imagination. So all mammals have about same number of genes and only sequence of codons differ. And each of them give birth to a new born of the same variety. Very same yet 'different'individual. So function of genes is 'not' to determine color of eyes or hairs. It is there, but it is secondary. It has already performed some function and is performing the function not known. Then growth of the individual is decided by 'Genes'. When to get puberty, when to get adult, to produce offspring, when to get 'old' and when to die. This true for all living organisms and genes directs the formation of all of them.
(You have about 20,000 to 25,000 genes in all the cells of your nucleus. So when the zygote is formed in your body, one of the gene directs to form two cell stage. Then another gene directs to form four cell stage. Then again you have a gene to form eight cell stage. So suppose 'A' gene directs formation of two cells. Then gene 'B' will take over charge in one cell and gene 'C' will take charge in second cell. At four cell stage the charge will be handed over to genes 'D', 'E', 'F', 'G'. This way each division is directed by specific gene. Then next specific gene directs to form inner and outer cell masses. The role of each cell is decided by other specific gene which is assisted by other genes successively. The formation of third layer of the embryo is again decided by some specific gene. So you have permutations and combinations of genes to the tune of 20,000 * 19,999 * 19,998 * 19,997 * -------2*1. This is very large number and can decide the unique sequences of codons for the past and future, animals, plants as well as microorganisms also. ( Probably your personal computer will find it impossible to write down the actual figure with out the help of Log.) So with various permutations and combinations, each and every cell can be decided. You can take the example of cardiovascular system. You may have single precursor cell for the cardiovascular system. Then you have the single tube. From this single tube you get 'all' types of cells like SA node, atrial cells, AV node, bundle of His and ventricular cells.)

There is another angle to be explained. Like how do genes decide to form the individual species. It is the genes that form vertebrates versus non vertebrates. There has to be a gene or set of few genes to give rise to a vertebra in vertebrate animals. It is common to all the vertebrates. (A minor defect in this gene will give rise to a condition like spina bifida.) It should be absent in non vertebrates. So many genes in the vertebrates are common, till certain stage of development of the embryo. Then there is branching to decide if the animal be a mammal or not or like. A particular gene or set of few genes has to decide this. Then there has to be gene or set of few genes to decide if the animal will be a carnivore or a primate. There has to be a gene, which decide the further each and every segregation. Such segregation continues to the level of making every individual of the species to the unique features that one posses. Right up to the color of iris, for example.

So there is a gene, which decides that the individual belongs to the plant kingdom or animal kingdom. There is a gene, which decides if the animal will be unicellular or multi cellular. That means there is nothing like junk gene. It is your lack of knowledge to say that the particular gene is a junk gene. Most of the genes function for formation of the organisms. Once they have done this job. They remain silent. Every gene has to be there in the chromosomes. Otherwise the information of formation of the organism can not be transmitted to the next generation. Some genes perform primary function and others lead to further and further differentiation. Here the permutations and combinations of the genes is needed. Mutations occurs very commonly in the genes. Then such mutated individuals do not sustain. Most of the miscarriages takes place out of such genetic defects. Very rarely a new species is formed out of such mutation.

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