The first thing any embryo must do before it can develop into an organism is establish early polarity—that is, it must set up a way to distinguish its top from its bottom and its back from its front. The mechanisms that establish the earliest spatial configurations in an embryo are far less similar across life forms than those relied on for later development, as in the formation of limbs or a nervous system: for example, the signals that the developing fruit fly uses to know its front end from its back end turn out to be radically different from those that the nematode, a type of worm, relies on, and both appear to be quite different from the polarity signals in the development of humans and other mammals.

In the fruit fly, polarity is established by signals inscribed in the yolklike cytoplasm of the egg before fertilization, so that when the sperm contributes its genetic material, everything is already set to go. Given all the positional information that must be distributed throughout the cell, it takes a fruit fly a week to make an egg, but once that well-appointed egg is fertilized, it is transformed from a single cell into a crawling larva in a day. By contrast, in the embryonic development of certain nematodes, the point where the sperm enters the egg appears to provide crucial positional information. Once that information is present, little bundles of proteins called p-granules, initially distributed uniformly throughout the cytoplasm, begin to congregate at one end of the yolk; when the fertilized egg divides, one of the resulting cells gets all the p-granules. The presence or absence of these granules in cells appears to help determine whether their subsequent divisions will lead to the formation of the worm's front or back half. A similar sperm-driven mechanism is also thought to establish body orientation in some comparatively simple vertebrates such as frogs, though apparently not in more complex vertebrates such as mammals. Research indicates that in human and other mammalian embryos, polarity develops much later, as many stages of cell division occur with no apparent asymmetries among cells. Yet how polarity is established in mammals is currently a tempting mystery to researchers.

Once an embryo establishes polarity, it relies on sets of essential genes that are remarkably similar among all life forms for elaboration of its parts. There is an astonishing conservation of mechanism in this process: the genes that help make eyes in flies are similar to the genes that make eyes in mice or humans. So a seeming paradox arises: when embryos of different species are at the one- or few-cell stage and still appear almost identical, the mechanisms of development they use are vastly different; yet when they start growing brains or extremities and become identifiable as distinct species, the developmental mechanisms they use are remarkably similar.