2  The term eukaryote refers to a cell with the presence of a membrane-bound nucleus.  Any cell nucleus whether or not it is membrane-bound is essentially the intelligent center wherein information for the nucleotide sequences comprising the proteinaceous constituents of cell structures and functions are encoded.  In contrast to the eukaryotes, the prokaryotes are organisms whose nuclear material is itself not bound by an integral membrane.  The attempt to accomplish a phylogenetically correct and simple division of domains in order to classify all extant living organisms by the categories of prokaryote versus eukaryote is not valid; this remains a complex biological question.  In order to better understand how to regard the vast diversity of living things in biological science which is fundamentally a science that had been born of classification by the ancient Aristotle, tracing briefly the historical ideas of how to classify living things should be most useful.  With the growth of knowledge in biological science, the classification of organisms which had begun as a grosser level natural science has turned out to be an invaluable tool for unraveling the evolutionary history of living things since it traces living beings through groupings which converge on common ancestry.  This mapping backwards to common ancestors maps out an evolutionary root for all of the various species.  

There is an inquiry which can be posed in biology which is more pertinent to all of evolution than any other inquiry can be by its nature; the nature of this inquiry is so all-encompassing to the study of life that if it is ever answered definitively in some way, then the actual theory of evolution could then graduate to a law, perhaps.  That life had evolved from some primordial sea of chemicals covered by a vaporous canopy of a gaseous mixture of unknown constituency is one question.  However, the means to answer this question are greatly diminished when compared to the power to speculate upon the topic.  That life had once ever individuated, however, can be  answered  readily in the affirmative; indeed, even a rock has a place, even inert matter located in the crust of the earth is involved in some way with the animated ones who rely upon such firmament directly.  The identity of the living thing is typically referred to as the self of that living thing.  As biologists probe empirically into  the inner workings of an organism, the entire exploration is conducted, indeed, with the approach that there is a dominion of life at hand whose identity can  be tested in some way using various parameters.  One profound respect for the nature of life draws upon the fact that each and every organism defines its survival since it can react and interact with its environment and with other organisms of all kinds, not only its own, with a strict sense of identity.  This identity can express in many ways -- biochemically, reflexively, tactilely, phototropically, or in any given manner of sensitivity which can be named endlessly and empirically discerned -- and this individuation of life is usually implicit in our understanding of life.  Yet, if one were to survey the branches of biological science in seeking for a way to best grasp life itself for its essential nature scientifically somehow, some might be satisfied intellectually with chemical equations, some with studies of behavior in sentient beings, or others with problems of ecology; still others would try to find some unifying feature or factor which could summon forth all of the knowledge of chemistry, mathematics, and physics as applied to the study of life in a way which would have the greatest meaning.  That fundament should be found firmly in the study of the cell. //                  

In the 1700s Carolus Linnaeus of Sweden had set forth the taxonomic classification of living things according to whether they were plants or animals.  Each organism was to be named binomially by its genus and species so that the greatest degree of commonality of traits would be certain to resolve into a recognizable group identifiable even visually as a certain species.  Indeed, this guiding categorization of living things set forth by Linnaeus carried on well into the 1900s even as cytology and microscopy had expanded the knowledge of life unto the biochemical and molecular levels.  As Linnaeus's work was extended into biological classification, the animal kingdom was thought to include the protozoa, and the plant kingdom was to have included the bacteria.  However, the binomial system for classification which Linnaeus developed had preceded the emergence also of evolutionary theory in biological science.  He of course had worked from the gross level of observation of morphological characteristics as he worked to classify organisms.  Since evolutionary thought is nowadays so fundamental to the biological understanding of life, it was inevitable that a system of classification of living things would ultimately come into force which could work at least from the molecular level of traits in proving organismal relationships.  This change in biological thought towards classification can be derived from the role of the genome of the cell whose replication mode through the DNA of the genome preserves the passage of life onto the next generation through its replication as well as through repair mechanisms -- the genetic code is indeed a code which is smart unto itself even beyond replicative abilities; the genome further becomes the source of variation in genetic code, the mutation, wherein repair of alterations as a built-in smart feature happens to be imperfect.  Genes which escape repair can prove to be vital for a population of organisms striving to survive. That is, mutational changes expressed phenotypically can bring about the natural selection of new traits in the Darwinian paradigm for evolutionary change. 

In 1969 there came about a new system of classification through the publication by Robert Whittaker (1) wherein five kingdoms of living things were named: plantae, animalia, protista, fungi and Monera (bacteria and blue-green algae.)  Whittaker wished to add a fifth kingdom to his earlier work of 1959 wherein there had been named four classificatory kingdoms (2); this fifth kingdom of Monera would set up a simplification of categorization based upon the presence or absence of a membrane-bound nucleus in the cell, that is, as according to prokaryotic or eukaryotic cell structure.  Thus, Whittaker added the kingdom Monera so as to include the prokaryotic bacteria most fundamentally as the prokaryotes.  

The theory of endosymbiosis holds that both bacteria and archaea had contributed to the eukaryotic cell as it had once evolved into a kind of cell with membranous compartments -- mitochondria and chloroplasts in addition to the nucleus.  The RNA of ribosomes in eukaryotes, for instance, actually resembles by genetic code sequence a sequence closer to archaea than to bacteria.  This contributes to evidence that archaea had through endocytosis been integrated into the life of some prokaryotic precursor to the eukaryotic cell at some point in evolutionary history; the Serial Endosymbiosis Theory (SET) involves a purported sequence of such endosymbiotic events between certain theoretical prototypes of cells with archael hosts and bacterial vectors, for instance, which had sequentially evolved into the eukaryotes of higher plants and animals as we know of them.  Evidence suggests that bacterial symbiosis with a eukaryotic precursor had brought about mitochondria and chloroplasts.  These membrane-bound organelles have their own protein synthesizing machinery with which the nuclear genome cannot correlate for synthesizing new mitochondria and chloroplasts.  Therefore, these organelles can only be formed from such that already exist by fission.  However, this functional delimitation of the nucleus such that it does not carry the code for replicating two of its organelles stations the nucleus of the cell at a provisionary loss in reference to the powerhouse of the cell, the mitochondria, and to the food manufacturer, the chloroplast; the nucleus simply cannot produce all of the proteins of which these organelles are made.  Indeed, mitochondria and chloroplasts with their own genomes replicate their DNA in a way similar to bacteria.  Indeed, were these organelles once themselves living, bacterial organisms?

Since they both concern the metabolic functions involving the energy use which universally supports the thriving life of any organism, the energy governance that the mitochondrion effects and the energetic food source of the chloroplast of plant cells might be expected to have their genetic inheritance as according to their own unique, integral lineage within the genome of the cell -- the DNA of the nucleus of eukaryotes or of the nucleoid of prokaryotes; accordingly, the vital function of energetic events in the organism should be encloistered, one would think, cordoned off somehow so that the struggle for preservation of ongoing life would be that much more secure.  Therefore, would not the metabolic machinery of the cell as it evolved across great time be greatly conserved genetically compared to all other structural entities of the cell?  The Darwinian concept of natural selection spawned evolutionary theory, yet Darwin's conceptual work was drawn from macroscopic empirical observations.  Having drawn a guiding concept towards evolution as that of the longevity not even of the individual organism, but of populations of them as he had extended the mathematical predictions of Malthus regarding how geometrically increasing populations contend for a lesser, arithmetically increasing food supply, Darwin drew up the mathematical matrix for similarly for species at the population level.  Therein, changes in traits of species could gain genetic supremacy and become conserved through the process of natural selection.  This mode of species evolving through the process of natural selection concerns essentially the life  of the organism still held as against the external world even though it is figured in the larger numbers of groups of them or of populations.  The source of variation is from the internal -- the genome -- which mutation then is related to the external world for testing.  The genetic infusion of the symbionts thought to guide cellular evolution as to its structure, on the other hand, is an externally born event of one living organism to another.  This binding of life to life on the behalf of survival stands in contrast to life versus world in a fundamental sense; what further cannot evade mention is astounding: whereas populations of organisms in order to qualify for evolutionary level change in the status of varied traits strive most essentially for the substance of survival as per food, the symbiosis of, say, an oxygen-respiring bacterium settling in a prototypic anaerobic host lends its being towards aerobic respiration to cause the creation of a mitochondrion within the host cell.  This is the provision at the cellular level through horizontal genetic transfer of the fuel for ongoing life and survival -- energy; energy is produced at the molecular level in the mitochondrion through the process of respiration most efficiently.  This commerce of energy is part and parcel of the living thing; it is ubiquitous throughout the living world.  The efficient respiratory mechanisms of the mitochondria centralize the metabolism of the cell so that its essential interface with the external world is changed drastically enough to allow cells to then specialize unto aggregate beings, now multicellular in nature.   Whereas a simple bacterium may gain the molecules it needs for sustenance from an abundant supply in its environs, as life evolved cellularly the relationship with the external world of even slightly higher order cells must have seen an altered picture regarding food source and therefore the chemistry of energetic processes for sustaining life.       

That the provision of organelles functioning as powerhouses of the cells might well have a symbiotic origin genetically should ultimately expand our understanding when this origin is more succinctly traced.  Such confluent genetic influence of both archaea and bacteria in the formation evolutionarily of the eukaryotes as according to the endosymbiotic theory constitutes a horizontal gene transfer rather than a vertical gene transfer.  In a vertical gene transfer, there would have been the influence of a gene mutation which had taken the lead in the Darwinian sense of survival of the fittest in a particular genetic diversity; such a mutation would have contributed accordingly to the evolution of multi-cellular beings which are comprised of eukaryotic cells.  Instead of this vertical transfer, the horizontal transfer of genes just described could have occurred wherein existing prototypes of a new order of life would have been infused with a genetic resource formed at the level of the phagocytosed entities named, archaea and bacteria.  The endosymbiotic theory of the evolutionary formation of eukaryotic cells is still being sought out for firmer verification.  Indeed, the rise of the entity of the eukaryotic cell in the history of life is thought to be of paramount importance; the rise of eukaryotes not only could have allowed multicellularity to gain precedence among living things, it also could have matched or possibly help implement the chemical attributes of the global environment from an anaerobic to an aerobic nature.  If life is essentially the ability of an organized entity to take inert constituents from the world surround and convert them into use within so that energy is utilized most efficiently, and if such life must also possess the ability to self replicate, then would this life in another geologic time of the earth actually be able to exert the power collectively through its energy commerce with the inert chemicals present in, on and around the earth to effect a change in the atmospheric content from carbon dioxide and nitrogen into oxygen?  If this is better understood, them perhaps a more educated approach to our current day ecological needs might allow technological advances to be addressed more intelligently; we do consume a finite amount of fossil fuel present here geologically, and the burning of this fuel as well as the prevalence of chemical waste of the industrial complex are leading concerns now for the health of the environment about us. 

(1)Whittaker RH (1969) New concepts of kingdoms of organisms. Science 163:150-160

(2)Whittaker RH (1959) On the broad classification of organisms. Quart Rev Biol 34:210-226