Synthetic biology

“ On the one hand, if tacit knowledge remains important in synthetic biology, then this implies that it will not be easily accessible to outsiders and this reduces concerns about the dual-use threat. On the other hand, if synthetic biology is an engineering discipline and if, as stated by Mukunda et al. ”

“ Results Myth 1 Synthetic biology is de-skilling biology and making it easier for terrorists to exploit advances in the biosciences
Founding leaders in synthetic biology have argued that developments in the field would lead to a situation where biology would not only become “easier to engineer,” but that it would become easier for anyone to engineer biology. ”

“ To say, as above, that complete molecular homogeneity existing among the members of a species, must render impossible that mutual molecular disturbance which constitutes fertilization, is but another way of saying that the actions and re-actions of each organism, being in perfect balance with the actions and re-actions of the environment upon it, there remains in each organism no force by which it differs from any other—no force which any other does not meet with an equal force—no force which can set up a new evolution among the units of any other. ”

“ They operate entirely within the framework of natural laws, and can only utilize what energies are available for them at the given time and place. Every cell has its dominants; and as an [Pg 122] organism is a synthesis, not a mere aggregate, of cells, so its individual dominant is a synthesis of the dominants of its parts. The evolution of species, like the development of an embryo, is under the control of dominants. ”

“ Genes can survive only by coding for real physical structures of interacting macromolecules, whose evolution can and must be studied by transition analysis of their phenotypes, not just of their gene sequences. ”

“ Hence, then, there is congruity between the above interpretation and certain general truths displayed by animal organization at large. We may infer that in a way parallel to that just indicated, cell-evolution was, under one of its aspects, a change from a stage in which the exciting substance and the substance excited were mingled with approximate uniformity, to a stage in which the exciting substance was gathered together into the nucleus and finally into the chromosomes: leaving behind the substance excited, now distinguished as cytoplasm. ”

“ Such a phylogenetic accumulation in these low types of moments is formed only by variation and natural selection, while in the case of the synthetic moment the accumulation is formed during the life history of the particular individual. ”

“ And we need not therefore be surprised to find, as we do find, specks of protoplasm manifesting life, and yet showing no signs of organization. A further stage of evolution is reached when the imperfectly integrated molecules forming one of these minute aggregates, become more coherent; at the same time as they pass into a state of heterogeneity, gradually increasing in its definiteness. That is to say, we may look for the assumption by them, of some distinctions of parts, such as we find in cells and in what are called unicellular organisms. They cannot retain their primordial uniformity ”

“ Not only the established truths of Biology, but the established truths of science in general, negative the supposition that organisms having structures definite enough to identify them as belonging to known genera and species, can be produced in the absence of germs derived from antecedent organisms of the same genera and species. If there can suddenly be imposed on simple protoplasm the organization which constitutes it a Paramœcium, I see no reason why animals of greater complexity, or indeed of any complexity, may not be constituted after the same manner. ”

“ An animal or plant in which the chromatin is unequally divided among the cells, must have tissues of uncertain formation. Assume that an organ has, by survival of the fittest, been adjusted in the proportions and qualities of its parts to a given function. If the multiplying protoplasts, instead of taking equal portions of chromatin, have some of them smaller portions, the parts of the organ formed of these, developing less rapidly and having inferior energies, will throw the organ out of adjustment, and the individual will suffer in the struggle for life. ”

“ In short, gene losses and quantum evolution of sequences beyond recognition grossly distort such statistics. We must consider bacterial evolution as a problem of organismal evolution and not base conclusions only on the sequences of the non-representative minority of genes that evolved sufficiently trivially to still allow sequence alignment and tree making. ”

“ Evidently organic evolution, whether individual or general, must always and everywhere have been subordinate to these physical necessities. Though natural selection, beginning with minute portions of protoplasm, must all along have tended to establish a molecular composition apt to undergo this differentiation of surface from centre to the most favourable extent, yet it must all along have done so while controlled by this process of direct equilibration. ”

“ Speculation aside, however, we may say that the two functions of the chromatin do not exclude one another, but that the general activity which originates from it may be but a lower phase of that special activity caused by fertilization. [2]
§ 74g. Here we come unawares to the remaining topic embraced under the title Cell-Life and Cell-Multiplication. We pass naturally from asexual multiplication of cells to sexual multiplication—from cell-reproduction to cell-generation. The phenomena are so numerous and so varied that a large part of them must be passed over. ”

“ Thus the hypothesis of evolution prepares us for those two radical modifications of the cell-doctrine which the facts oblige us to make. It leads us to expect that as structureless portions of protoplasm must have preceded cells in the process of general evolution; so, in the special evolution of each higher organism, there will be an habitual production of cells out of structureless blastema. And it leads us to expect that though, generally, the physiological units composing a structureless blastema, will display their inherited proclivities by cell-development and metamorphosis ”

“ It is a basic fallacy to regard bacteria or eukaryotes as being simply the product of their genes and genomes. Genes can do nothing outside this structural framework. It is not clear even in theory how lateral gene transfer could cause a structural innovation like the origin of thylakoids or the addition or loss of an outer membrane. To use the word phylogeny to apply just to gene sequence trees is, as you candidly admit, a too narrow interpretation. One must consider structures and morphogenesis as well as genes in phylogeny. ”

“ When we thus see the identity of method at the two extremes—when we see that the general laws of evolution, as they are exemplified in known organisms, have been unconsciously conformed to by chemists in the artificial evolution of organic matter; we can scarcely doubt that these laws were conformed to in the natural evolution of organic matter, and afterwards in the evolution of the simplest organic forms. ”

“ We realize now the difference between the moment of the desultory type and the moment of the synthetic type. The desultory reproductive moment is highly stable in its organization, formed by variations and the iron hand of natural selection; it is crystalized in character, function does not effect its organization. The reproductive moment of the synthetic type, however, while having on the one hand as its basis a functioning apparatus, formed in the course of phylogenesis, has on the other hand a large capacity for modification, and is mainly built up by function ”

“ Seeing, on the one hand, that gamogenesis recurs only in individuals which are approaching a state of organic equilibrium; and seeing, on the other hand, that the sperm-cells and germ-cells thrown off by such individuals are cells in which developmental changes have ended in quiescence, but in which, after their union, there arises a process of active cell-formation; we may suspect that the approach towards a state of general equilibrium in such gamogenetic individuals, is accompanied by an approach towards molecular equilibrium in them ”

“ This is the fundamental cause of the fixity of species, which means the production of offspring having the same specific characteristics as their parents. How, under these conditions, the mutability of species is brought about must be discussed later. It is first of all necessary to inquire more closely into the composition of the chromatin, and to study the special phenomena of cell-growth in connexion with conjugation, where new and extraordinary features come to light.
A chromosome is not, or is not usually, a simple body. ”

“ Now, it is the union of germ-plasms which is required to reproduce new individuals of multicellular organisms that determines congenital variations on the part of such organisms, and thus furnishes natural selection with the material for its work in the way of organic evolution—work, therefore, which is impossible in the case of unicellular organisms, where variation can never be congenital, but always determined by the direct action of surrounding conditions of life. ”

“ Besides insuring a structural fitness between each kind of organism and its circumstances, the working of "natural selection" also insures a fitness between the mode and rate of multiplication of each kind of organism and its circumstances. We may, therefore, without any teleological implication, consider the fitness of homogenesis and heterogenesis to the needs of the different classes of organisms which exhibit them. ”

“ Throughout my argument the implication everywhere is that the physiological units are all of one kind; whereas Mr. Darwin regards his component units, or "gemmules," as being of innumerable unlike kinds. He supposes that every cell of every tissue gives off gemmules special to itself, and capable of developing into similar cells. We may here, in passing, note that this view implies a fundamental distinction between unicellular organisms and the component cells of multicellular organisms, which are otherwise homologous with them. ”

“ Such a realization correlates well with our understanding of molecular evolution, which often obliterates easily recognizable sequence similarity among genes that diverged a long time ago, but leaves behind traces of statistically significant patterns of conserved residues that are apparent only when multiple, related sequences are aligned. ”

“ Idio-plasm-B is the substance out of which future cells are to be formed and controlled, when in due course either of ontogeny or phylogeny this idio-plasm-B becomes converted into idio-plasm-A,—i.e., into each subsequently developing tissue or organism, as the case may be. I say ontogeny or phylogeny, and tissue or organism, because, where a germ-cell is concerned, idio-plasm-B is capable of reproducing entire organisms of its own and of subsequent generations ”

“ XIV, that an essential characteristic of Evolution is the integration of parts, which accompanies their differentiation—an integration shown both in the consolidation of each part, and in the union of all the parts into a whole. Hence, animate bodies having greater co-ordination of parts than inanimate ones must exhibit greater co-ordination of changes; and this greater co-ordination of their changes must not only distinguish organic from inorganic aggregates, but must, for the same reason, distinguish higher organisms from lower ones, as we found that it did. ”

“ If the germ-plasm be a system of determinants, then the same laws of struggle for existence in regard to food and multiplication must hold sway among its parts which hold sway between all systems of vital units—among the biophors which form the protoplasm of the cell-body, among the cells of a tissue, among the tissues of an organ, among the organs themselves, as well as among the individuals of a species and between species which compete with one another. ”

“ A Protozoön (like a Protophyton) is a solitary cell, or a “unicellular organism,” while a Metazoön (like a Metaphyton) is a society of cells, or a “multicellular organism.” Now, it is only in the multicellular organisms that there is any observable distinction of sex. In all the unicellular organisms the phenomena of reproduction appear to be more or less identical with those of growth. Nevertheless, as these phenomena are here in some cases suggestively peculiar, I will consider them more in detail. ”

“ In Heterogenesis, on the other hand, we have the birth of dissimilar products, the beginning of a new branch from a "life-tree," in which the offspring have no tendency to assume the parental type. This occurs, for instance, where the protoplasmic matter of an animal or of a vegetal cell becomes modified and resolved into Bacteria. ”

“ The suspected role of DNA in information storage and the development of new concepts of the coding mechanism in DNA that may lead to a universal biological theory embracing evolutionary, as well as homeostatic, adaptation to environment and learned behavioral systems
With the essential biochemical constituents of life and the mechanism of replication beginning to be understood, the challenge for the synthesis of living matter by abiogenic experimental techniques has become to many scientists the ultimate goal of the scientific era. ”