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Literal miniature-organism theories had lost their former standing, but the explanatory problem had been transformed rather than abolished. By 1900, arguments about inherited organization, cellular differentiation and the response of an embryo to intervention were central to embryology. These were recognizably related to the older contrast between preformationism and epigenesis, even though neither eighteenth-century label could be carried unchanged into the new work.

The basic distinction concerned how organization arose. In preformationism, development unfolded organization already present in the germ; an increase in visible size did not require the original construction of the organism's arrangement. Epigenesis treated organs and differentiated structures as arising progressively. These broad positions left many further questions open. A claim that new visible organs appeared did not itself explain the material conditions that generated them, while a claim about inherited organization did not necessarily require a fully formed microscopic adult. Failure to separate these levels makes an apparent victory over the crudest miniature-organism picture look like the solution of every developmental problem.

August Weismann's discussion supplies contemporary evidence that the old opposition remained analytically useful in altered form. In the 1889 Essays upon Heredity and Kindred Biological Problems by August Weismann, he distinguished older miniature-animal preformationism from more recent accounts involving organized hereditary material. He discussed Charles Darwin's pangenesis under the latter category. That classification is not a claim that Charles Darwin literally believed in a tiny complete adult: it identifies a theory in which material representatives of parts contribute to the germ. The same discussion contrasted this with an epigenetic process in which an initial material constitution generates successive developmental states.^[ref]

August Weismann's germ plasm also relocated the problem of continuity between generations. A continuity of hereditary material could distinguish reproduction of the lineage from changes acquired by the body. But identifying continuity did not by itself establish how different parts of an embryo received different developmental capacities. A hypothesized partition of hereditary determinants during successive divisions offered one possible explanation. That possibility could be investigated by intervening on an embryo, rather than only inspecting it with an optical microscope.

The contrast between Wilhelm Roux and Hans Driesch makes the continuing issue concrete. In the frog experiment published in 1888, Wilhelm Roux killed one of the first two blastomeres with a heated needle and observed development of a partial embryo from the survivor. The result suggested mosaic development: an early part might possess a restricted developmental contribution. It did not, without further assumptions, identify a particular material in the nucleus as the cause. Nor was killing a cell and leaving it in place equivalent to cleanly separating the two living cells.

In trials begun in 1891, Hans Driesch separated or isolated early sea-urchin blastomeres; some developed into smaller but whole larvae. This supported regulative development and contradicted the claim that the first division universally and irreversibly partitioned the capacities required for different halves of the animal. The different animal, manipulation and surviving material mattered. One could not infer from the contrasting outcomes alone that one investigator had simply observed correctly and the other incorrectly.^[ref]

These experiments did not prove an absence of structure in the egg, and they did not establish that every embryonic cell retained every developmental possibility at every stage. Regulative development can depend on existing organization and interactions. Equally, Hans Driesch's eventual advocacy of vitalism was an interpretation of the findings, not an observation directly forced by a whole larva. The source cited here is his 1908 retrospective of pre-1900 work; its later philosophical formulation must not be silently treated as the precise position held at the original trials.

The debate had therefore become irrelevant only in a narrow sense: the old binary, if taken to mean a tiny complete organism versus the production of organization from wholly unstructured matter, no longer adequately described the best questions. In a broader sense it remained active as a dispute over what was inherited, what became progressively determined and how parts depended on the whole. The emergence of experimental embryology changed the evidence by which those claims could be tested. It did not make the relation between heredity and biological development disappear, and it should not be redescribed using modern epigenetics as though that were simply a new name for historical epigenesis.

Nineteenth-century embryology transformed knowledge of reproduction from an account of fluids and visible growth into an increasingly cellular account of fertilization and biological development. It did not end with a complete mechanism of heredity. The century must be treated as a changing sequence: what was established by the 1890s cannot be attributed without qualification to an investigator in 1800. The key changes concerned the material contributions of the parents, the origin of embryonic structures and the evidential power of observation versus intervention.

An early problem was identifying the mammalian ovum. A large ovarian follicle is not itself the ovum, and failure to distinguish the two could confuse the material starting point of biological development. In 1827 Karl Ernst von Baer described the mammalian ovum, notably from the dog, in De ovi mammalium et hominis genesi by Karl Ernst von Baer. Dissection located the relevant structures; optical microscopy distinguished the small ovum within the follicle. The evidence was therefore a combination of anatomical placement and magnified appearance. The work's title must not be taken as proof that he directly observed every corresponding stage in human reproduction.^[ref]

This mattered to the contest between preformationism and epigenesis. If the embryo were already a tiny formed individual, growth would chiefly enlarge structures already present. Successive observations of incubated eggs instead showed structures appearing and differentiating over time. Serially examining embryos at different stages made an ordered developmental account possible; it did not normally follow the same opaque mammalian embryo continuously from beginning to end. Nor did rejection of a miniature adult settle every question about invisible inherited organization. An investigator could accept the visible emergence of structures yet propose pre-existing determinants below the resolving power of the optical microscope.^[ref]

During the century, cell theory and improved techniques made cell division a central explanatory object. Lenses, illumination, thin sections, fixation and staining helped observers distinguish cell nuclei, chromosomes and patterns of division. These were achievements of preparation as well as magnification: a preparation could preserve a fleeting structure but also distort it. Comparing preparations and checking fixed material against living specimens were therefore important safeguards. By the late century, a developmental sequence could be described as successive divisions and rearrangements of cells, rather than the spontaneous appearance of a fully organized body from undifferentiated fluid.^[ref]

Fertilization became a particularly revealing test. External fertilization in transparent marine eggs allowed investigators to mix sperm and unfertilized ova at a known time and watch the sequence under an optical microscope. Oscar Hertwig's sea-urchin investigations in the 1870s connected sperm entry with the appearance and union of the male and female nuclear contributions before the first cleavage division. His later The Cell by Oscar Hertwig presents these events as central to the process. Separating eggs from sperm, observing them before mixing, and comparing the sequence after mixing could distinguish fertilization from ordinary changes in an ageing egg. Serial nuclear observations supplied evidence about what entered and what happened next, not merely a correlation between mating and later offspring.^[ref]

Nevertheless, fusion of parental nuclear material did not reveal the modern molecular mechanism of heredity. Chromosomes supplied observable structures whose behavior could be compared across cell divisions, and the contributions of the two gametes could be investigated. This is different from knowing that DNA encodes information in a particular nucleotide sequence, or knowing how that information directs development. Even the apparent continuity or disappearance of a cell nucleus during division was a historically difficult observational problem. The distinction between a visible structure and the theoretical function assigned to it is essential.^[ref]

The final decades added experimental embryology. In 1888 Wilhelm Roux injured one of the first two blastomeres of a frog embryo with a heated needle; partial development of the survivor appeared to support a mosaic theory of development, in which early divisions distribute distinct developmental capacities. In 1891 Hans Driesch separated early sea-urchin blastomeres by shaking and found that an isolated blastomere could form a small complete larva. That showed a regulatory capacity inconsistent with an exclusively rigid allocation of half the future organism to each of the first two cells.^[ref]

The comparison requires care: killing a cell and leaving it attached is not the same intervention as removing it, and a frog is not a sea urchin. The results therefore did not establish that all embryos develop identically or that every early cell can make an entire organism. They did establish that a normal developmental fate cannot automatically be equated with an irreversible developmental capacity. Hans Driesch's later commitment to vitalism was one interpretation of this capacity, not something a complete larva logically proved. His 1908 retrospective account is valuable participant evidence, but it is later than the nineteenth-century trials it describes.^[ref]

By the century's end, investigators had strong evidence for the cellular starting points of sexual reproduction, parental nuclear participation in fertilization and active organization during biological development. They knew these things through dissection, prepared and living microscopic observations, comparison of stages, and increasingly discriminating interventions. Their continuing uncertainty about heredity and developmental organization was productive: it concerned mechanisms that their best observations had made more precisely questionable, rather than a simple absence of facts.