During the Age of Enlightenment, speculations arose as to the origin, structure and function of “spermatic animalcules”: whether they really exist, whether the tail has any function, and whether they are molecules representing a transition from non-living molecules to life, tiny animals with complex organs or perhaps tiny people. Eventually, scientists found that they have no internal organs, cannot multiply and that they are normal constituents of the male organization. Anatomists could not explain the formation of complex embryos from featureless eggs and semen. How does Matter gain Form? The Epigenesis theory argued that development progresses gradually, from unorganized egg materials to organized structures, by successive building of organs. The power of embryogenesis is in Matter itself, which gains Form. The Preformation theory believed that Form comes before Matter. This theory required no intra-matter formative powers. God had formed all future generations of all living creatures during Creation as miniature versions of themselves. Embryonic development occurs through the expansion and growth of these preformed miniatures, and future potential creatures await the time to develop into actualized creatures when God so wills. Parthenogenetic aphids seemed to prove that the preformed embryo was in the female gamete; other evidence suggested it was in the semen. Enlightenment naturalists thought that organisms develop from preformed germs consisting of inert, folded nets that expand when activated by fertilization. God can change species’ germs so that they would reach higher perfection levels, just like embryos that develop into higher stages. Death is a metamorphosis to a future existence (resurrection), with indestructible soul germs surviving death, rising from the dead and dwelling in bodies of higher animals—repeated rebirth with perfection, up the ladder of nature. Nature’s ladder places simple organisms at the bottom and complex ones at the top in a hierarchy of increasing body complexity and perception powers. Individuals reach perfection through ontogeny, as they develop to higher states of complexity and perfection, mirroring this ladder. Palingenesis follows global catastrophes that destroy all body germs: the soul germs survive, enabling animals to reappear when Earth is again habitable. Each germ then develops into a new, more perfected organism, and all groups change simultaneously. Every soul has reincarnated several times, in different bodies and epochs. Some naturalists rejected preformation, suggesting that the need to satisfy lust, hunger and security determines diversity. All living creatures have descended from a single ancestor, with diversity rising from different responses to different stimuli. In classifying diversity, traditional theory maintained that each kind of plant and animal must have a defining essence. New theories claimed that information on essences is not reliable, and such classifications actually rest on indirect knowledge of secondary qualities. As essences are unobservable, we must make do with derived, observable features. As no observable feature is more indicative than another one, our classifications are arbitrary, only possibly conforming to real essences. Even at the real essence level, boundaries between species may be continuous rather than sharp, making it impossible to find boundaries of species on the observable level. Lacking knowledge of the essence, we should replace the traditional principle of using a single feature all the way down by using any of several observable features. These two rival theories resulted in very different, rival classifications. Linnaeus believed that information gained from the senses is valid and reliable for classifying nature and that essential features, alongside other features, are available for classification. Naturalists must present clear and distinct verbal descriptions—the clearer and more distinct our ability to distinguish and understand, the greater the degree of certainty. Nature forms a natural ladder, rising from minerals through plants to animals, among whom man ranks the highest—God has progressed gradually, from simple to complex. Linnaeus based his classifications on very few external features (even just one). Within a kingdom, he adopted a concise, uniform hierarchy with only four ranks for all minerals, plants and animals: class, order, genus, and species, thereby creating a four-tiered ranking system, as in the church, army and civil service. On his classification scale, he fixed the terms genus and species as absolute ranks, yet he emphasized that ranks were artificial devices to facilitate identification. He imposed on classification the obligatory use of a single pan-European language, Latin, and applied binomials to all three kingdoms, thereby giving nomenclature its simplicity and brevity and expressing the need to distinguish both the general and the particular. Linnaeus erred in assigning fossils to the mineral kingdom. Linnaeus believed that the mode of generation is a plant’s essence. He classified plant diversity by whether sexual organs are exposed or covered, whether stamens and style are on the same flower or not, whether separate from the style or fused and whether all stamens are equal or not. He next created classes by the number, shape and location of the male organs and orders by the female organ. Then he classified genera and species by other traits such as the root, stem and leaves; beyond this, he did not bounce between characters. This was, he believed, a natural classification, in contrast to not-natural, medical classifications. He classified animal diversity into six classes. Many of his orders were unnatural due to convergence. He listed only a few genera, perhaps believing that biblical Adam could memorize only a few names. Species are essential, unchanging entities created during Genesis; they cannot develop from other species and do not form spontaneously. In molluscs, he gave each genus one name characterizing its shell and a different name characterizing the animal inside the shell. Man is highly variable. Beyond mute, hairy savages, there are four races, one for each continent. They differ in colour, temperament and hair. Linnaeus, finding fossilized marine shells at mountaintops and thinking he had noticed a continuous retreat of the sea, considered this as evidence that land is continuously emerging. This suggested to him that in some past, the land was a small paradisiacal island with all today-existing habitats, and here God had created all creatures. As the island gradually emerged and grew, its creatures began dispersing into the new lands. The fossil beds on mountaintops were, he believed, remains of ancient shorelines of this island. Nature is harmonic and balanced, with every kind having its place in the web of life. God’s means of maintaining a balance is that predators daily destroy animals, which would otherwise multiply so rapidly as to deplete their own food sources. Furthermore, if all species inhabited the same place, some would dominate and eliminate the others. To prevent one species from displacing another, God had placed different species in different sites throughout the world. Furthermore, if one species over-multiplies and robs another species of its food, thereby introducing confusion into the harmonic balance of the world, God punishes it with sickness and death. Linnaeus was aware of the significance of biogeography, population dynamics and competition. Buffon followed the concept of relative time and space in organizing all quadruped diversity relative to a fixed, arbitrary reference point: man. We should study animals by the order in which they appear before us, beginning with the close ones. Accordingly, Buffon grouped all European domestic animals first, then European wild animals; he clustered Asian domestic animals separately. Naming all animals by their French common name, he followed the domestic animal series with a game animal series. His third series consisted of small carnivore pests. Hibernating quadrupeds were in a separate series. Then came species from other continents, broadly from the Americas, then Asia, then Africa (but with exceptions), and finally monkeys. He clustered seals, walruses and manatees by habitat. There were also attempts to erect natural clusters. Natural history became an additional element in Buffon’s species descriptions. It relied on documented observations, and these were often irregular, erratic, capricious and difficult to inspect, especially for animals in distant lands. Buffon erred in clustering all elephants into a single species, which he further erred by clustering also the fossil mammoths. These errors had consequences on his views on the origin of life. Hydra is a transitional creature, between plants and animals. It is green, lacks most animal organs and reproduces by budding; yet it moves, responds to touch and seizes and digests prey, thus suggesting a continuous plant–animal scale, not two distinct realms. When sliced up, hydra pieces regenerate complete individuals. Regeneration ability contradicts the Preformation theory: any claim that every tissue fragment contains a preformed embryo of the next generation is absurd; furthermore, animal regeneration is a new creation, occurring millennia after the biblical Creation. Regeneration also contradicts the belief in individuals possessing a material animal and an immaterial soul. In which of the new parts is the animal’s soul? Can a soul divide into many parts? If so, then is the soul merely a function of Matter? Enlightenment naturalists thought they had found that a “life force” exists, capable of spontaneous generation: new microscopic organisms develop in disorganized material and generate other microscopic creatures. Certain “primitive particles” are present in animals. When animals die, they separate but may rejoin and produce a new living entity. Later naturalists found flaws in these experiments and concluded that life is not only a feature of Matter. Linnaeus’ opponent was Buffon, who offered complete descriptions of animals, not telegraphic descriptions of external morphology. To determine the certainty of knowledge, he distinguished abstract from real knowledge. Abstract, mathematical truths are provable, but as they contain only what we put in them, they are useless in natural history. Physical truths rest only on facts of the real world. They consist of a series of similar facts, such as frequent and uninterrupted repetitions and orderly successions of the same events. Natural events that recur repeatedly are laws of nature. Buffon searched for basic laws in nature that would explain the beginning of the world and how life is generated. To explain the emergence of order out of chaos, he developed a secular history: a comet, hitting the sun, broke off debris, which eventually became the planets. Earth was at first a sphere of hot, melted matter; gradually it cooled and turned into dry land. Clouds then rained to form oceans, within which life spontaneously generated. Earth was then warmer than today, and the oceans once covered mountaintops; eventually, they receded, leaving marine fossils. Buffon suggested that indestructible “organic molecules”, through different combinations, create various species. An “internal mould” positions the molecules throughout the body, creating specific creatures and thereby giving empirical meaning to the species concept. Experiments (erroneously) suggested to him that microorganisms develop spontaneously from organic molecules. Microorganisms, intermediary between living and non-living, resemble natural machines in that they do not feed and do not generate ordinarily. In lower animals, upon death, the organic molecules set free, join other molecules and spontaneously reproduce. In higher nonsexual animals (plant lice), every organ sends molecules to a place where they reassemble, thus reproducing the parental internal mould. In highly organized creatures, sexual reproduction occurs. The molecules coalesce into a parent-resembling body under a Newtonian field of force, thus passing on the internal mould. The internal mould makes sense of species as genealogical entities, ensuring them as unchanging dynasties. Species fixity is a basic, universal law. If God were to destroy all living creatures, organic matter would form new internal moulds, resembling the old ones; also, on other planets, given proper conditions, the same species would appear. Buffon’s species were thus universal types of organic organization. Buffon rejected the Linnaean classification. Certitude about nature should rely upon real entities, not on abstract essences. In classifying, we need full descriptions, including internal morphology and full natural histories, not just external morphologies representing essences. Genus and order are meaningless ranks, and in practice, naturalists cannot agree on genus-level classifications. Basing life on reproduction, Buffon claimed that in nature, only one category exists, the species: a chain of similar, interbreeding individuals. A species is a system of concrete relationships between real entities. We recall a controversy on the nature of time and space in which Newton had claimed that these are absolute, abstract entities, whereas Leibniz claimed that without concrete things, there is no time or space. Buffon applied this time–space issue to biological classification: species exist only in the time dimension, in the destruction and renewal of creatures, and they are the only living entities in nature. Hybridization can determine whether individuals are of the same species. Beneath species, Buffon recognized varieties: lineages produced in response to changing environments. A permanent variety becomes a “race”. Buffon belittled racial differences in man, who forms a single, highly diverse species. Buffon eventually, encountering fertile hybrids and biogeographic variation, began doubting both fertility barrier absoluteness and species’ fixity. Animals change over time, and only the better-fitted survive due to natural selection. Consequently, animals cluster into genera and families, each with a single ancestor that has its internal mould. Ancestors may split into varieties, which sometimes hybridize. His earlier described species are mere races. Families are “expanded species” representing fixed moulds, whose products the environment may modify. Consequently, hybrids no longer ruin the reproductive criterion, domestic animals link to wild animals and fossils become ancient branches of a common root. The family should be the unit of classification, not the species. Buffon now established a new classification of quadruped diversity: non-splitting families versus splitting ones. A zoogeographic division, in both categories, included families of the Old World, both Worlds and the New World only. The American fauna suggests a continuum that once existed between the Old and New Worlds. Man is superior to all animals, and beyond him come grand, majestic animals. Birds also cluster into families, which he described without describing species. Buffon reached a far more detailed classification than did Linnaeus. Buffon described the history of nature in light of “historical knowledge”, differing from “physical knowledge” in that one reconstructs it. Throughout Earth’s slow cooling, oceans appeared and vanished, continents formed and sank and living beings came and went. Animals are perfectly adapted to the climate in which they were born, so as Earth slowly cooled, many animals could not adapt and went extinct. Extinctions release large quantities of molecules, and these, by spontaneous generation, build a new fauna, adapted to now lower temperature. Because of the limited amount of organic molecules, one animal wave must go extinct to enable the next wave to form. Temperature directs the organic molecule combinations, producing some animals rather than others. Animals may migrate, following a cooling climate, toward the equator; here, when the heat is no longer strong enough, they go extinct. In all places where the temperature is the same, one finds the same (or similar) plants and animals. Buffon’s history of Earth is, largely, a secular Genesis. Man is today transforming nature through land cultivation, domestication, swamp draining, forest clearing and other means. With our help, nature has reached today’s magnificent perfection.