That numerous chemical rearrangements of the atom - complexes take place outside the protoplasmic molecules - both of those left unemployed in assimilation and of those rejected during the destructive processes - will be readily understood: many of the bye-products found in plants, such as vegetable acids, alkaloids, colouring matters, crystalline bodies, etc., etc., are due to these, so to speak, fortuitous combinations and re-combinations.
The part played by respiration has often been misunderstood. It consists in the burning off of some of the carbon and hydrogen of the shattered protoplasm molecules, by means of the oxygen of the air, which finds its way into the fluids around the protoplasm, and when it is active every act of combustion - which is here an explosion - leads to the shattering of more protoplasm molecules, and consequently to more respiratory combustion of the products. If the supply of oxygen is limited the breaking down of the molecules of protoplasm does not cease, but the carbon and hydrogen which would otherwise have been oxidised are now in part left to form other compounds in the surrounding liquid, and thus incompletely oxidised bodies, such as vegetable acids, alcohols, etc., accumulate. Even in the complete absence of atmospheric oxygen the protoplasm may go on breaking down and accumulating various compounds containing relatively much carbon and hydrogen - so - called intramolecular respiration; but in ordinary plants this process soon comes to an end, because the blocking up of the molecular plexus leads to obstruction and interferes with the normal assimilation and dis-assimilation, and, if prolonged, leads to pathological conditions, and eventually death.
Here, then, we meet with a cause of disease, or of predisposition to disease. The deprivation of oxygen interferes with the normal processes of building up and breaking down of the protoplasmic molecules, and bodies we term poisonous accumulate and may lower the vitality or even bring life to an end.
During normal life other products of the disruption of the protoplasm molecules are nitrogenous bodies, such as proteids, and these we have reason to believe are used up again, acting as the nuclei, so to speak, of the new molecules, and so being built up again with fresh food-materials into the plexus, to be again set free, and again used up, and so on. Others are the carbohydrates, such as cellulose, which pass out of the molecule into an insoluble form, and are accumulated outside the protoplasm in the form of cellulose membranes, and so forth.
It is these formed products of metabolism (Metabolites), especially cellulose and bodies which result from its subsequent transformation, which constitute the main permanent mass of the ordinary plant.
We are now in a position to see how another fundamental cause of disease or predisposition to disease exists in the deprivation of the protoplasm of any of the elements needed to supply - in the food-materials - the place of those which have been permanently put aside in the form of cell-walls, or burnt off in respiration, passed out as excretions, or in other ways lost.
It is clear that the indispensability of an element must mean that the protoplasmic molecule cannot be completed without it: the same conclusion is supported by the experimental proof that these elements cannot be replaced by chemically similar elements.
It does not follow, however, that the protoplasm molecule must always have the same number of atoms of these elements, and grouped always in the same atom-complexes before being assimilated; nor that the protoplasm molecule, when once built up, always breaks down in exactly the same way. On the contrary, while the protoplasm of corresponding parts of a daisy and of a rose must contain all the elements named, we must believe that the atom groupings are different in the protoplasm molecule in each case; and though the molecules of the cell-protoplasm, of the nucleus, of the chlorophyll-corpuscles, etc., of one and the same plant must have all these elements, the atom groupings and modes of building up and breaking down may be very different in each case.
Again, the cell-protoplasm, bathed by the sap taken in by roots from the soil or fed directly by that derived from the leaves, must be exposed to very different stimuli and modes of nourishment, etc., from those incurred by the protoplasm of the nucleus which it encloses: and similar conclusions must apply in turn to the protoplasm of the root in the dark moist soil and of the leaf in the light dry air, or to that of the superficial epidermis cells as contrasted with that of the deeply immersed pith, and so on.
It is no doubt in these directions that we must seek for the explanation of many life phenomena at present quite beyond explanation. Thus, it is tolerably easy to modify the action of the cell-protoplasm of a plant, by exposing it to differences of illumination, temperature, moisture, and so forth, within certain limits; at least, since the changes in stature, tissue differentiation, cell-secretions, flowering capacity, etc., of plants affected by such factors of the environment - e.g. alpine plants brought into the plains - must be due to changes in the mode of activity of the protoplasm, we must assume that the above factors affect the latter. But it is extremely difficult to reach the nuclear-protoplasm directly by such stimuli, as proved by the experience that even where we allow the factors to act for a long time, no permanent change can be detected in the behaviour of the nuclear-protoplasm - the essential material in the reproductive organs and reproductive process. At least we must infer that no change has been permanently stamped on this nucleo-plasm from such facts as the characters of the seedlings of the progeny of the plain-raised plants: if they are again sown in an alpine situation they forthwith behave again as alpines.