Embryology and Development

Development is the process that builds an organism from a single cell. Because that process is inherited along with everything else, it preserves steps that no longer serve the adult animal — structures that form and then disappear, and genetic switches that still work when tested even though nothing uses them.

The evidence here is not that embryos of different species look alike. That claim was overstated in the nineteenth century and is dealt with below. The evidence is specific and testable: structures appearing in embryos that have no function in the adult but are functional in the adults of related groups, and developmental machinery that can be shown experimentally to still be present.

Structures that form and then vanish#

Whale and dolphin hind limbs. Modern cetaceans have no external hind limbs. Their embryos begin to grow them anyway. Thewissen et al. (2006) documented hind-limb buds in dolphin embryos that initiate normally and then arrest, and traced the arrest to the loss of Sonic hedgehog expression in the limb bud. The fossil sequence shows the same reduction over time.

Baleen whale teeth. Baleen whales have no teeth. Their embryos develop tooth buds, which are resorbed before birth, and the enamel genes are present as pseudogenes.

Snake limbs. Pythons and boas develop rudimentary hind-limb buds and retain a pelvic girdle and femur internally, with external spurs used in courtship.

Bird tails and teeth. Bird embryos form more tail vertebrae than the adult retains, and the surplus is resorbed into the fused pygostyle.

Human embryos. The human embryo forms a tail with a defined number of vertebrae that is largely reabsorbed, and pharyngeal arches that in fish become gill supports. These are covered in Atavisms and Vestigial Structures.

None of these structures is functionless in the embryo in every case — some contribute tissue to other organs. The point is narrower: they are built along a route that makes sense as an inherited path and not as a direct one.

The snake enhancer put back into a mouse#

The strongest recent result in this area is an experiment rather than an observation.

Limb development in vertebrates is controlled partly by a regulatory sequence called the ZRS, an enhancer that switches on Sonic hedgehog in the limb bud. Snakes still carry a ZRS, though they build no limbs.

Kvon et al. (2016) swapped the mouse ZRS for the ZRS from several species. Fish and human versions drove normal limb development. The python version drove reduced limbs. The version from advanced snakes such as cobras produced almost none — and when the researchers repaired a small deleted segment in the snake sequence, limb development was substantially restored.

The degradation is graded, and it is graded in the order the snake family tree predicts: pythons, which still have vestigial spurs, retain more function than snakes that have none.

An organism designed without limbs has no reason to carry a limb enhancer at all, and no reason for its degree of decay to track relatedness.

The same genes building different bodies#

Development is controlled by a small set of regulatory genes that are shared across animals separated by hundreds of millions of years.

Hox genes. Edward Lewis (1978) showed that a cluster of genes in Drosophila specifies which structure develops on which body segment, and that mutating them converts one body part into another. The same cluster, in the same chromosomal order, patterns the head-to-tail axis in vertebrates. The correspondence between gene order on the chromosome and position along the body is preserved across the animal kingdom.

Pax6 and eyes. Halder, Callaerts and Gehring (1995) expressed the mouse version of the Pax6 gene in fruit fly tissue and produced ectopic fly eyes on legs and wings. A mammalian gene triggered the construction of an insect compound eye — two eye types built from different tissues, sharing the master switch that starts the process.

Fins into limbs. Nakamura et al. (2016) used cell labelling and gene knockouts in zebrafish to show that fin rays and tetrapod digits arise from the same cell populations under the same Hox control, connecting the genetics to the fossil sequence from lobe-finned fish to early tetrapods.

This is "deep homology": not that the structures look alike, but that the machinery building them is the same inherited toolkit, repurposed.

Common objections#

"Haeckel faked his embryo drawings"

Largely accurate, and the criticism came from biologists. Ernst Haeckel's 1874 illustrations exaggerated similarity between vertebrate embryos, and his slogan that "ontogeny recapitulates phylogeny" — that embryos replay their adult ancestors in sequence — is rejected by modern biology.

Michael Richardson and colleagues (1997) photographed embryos across vertebrate species and documented how much the drawings had smoothed over, and Jonathan Wells built a chapter of Icons of Evolution on the episode.

Nothing above depends on Haeckel. Dolphin limb buds, snake ZRS enhancers, and Pax6 transplants are results from the last thirty years, obtained by sequencing and experiment rather than by drawing.

What has survived scrutiny is narrower and better supported: the developmental hourglass, in which vertebrate embryos are most alike at a mid-development stage and more divergent both before and after. Irie and Kuratani (2011) tested this against gene expression data across vertebrates and found the constraint concentrated at that stage.

"Similar development just reflects a common designer"

It accounts for shared functional machinery. A designer might reasonably reuse an eye-specification gene.

It does not account for construction routes that are longer than necessary, or for machinery retained where nothing uses it. A whale embryo does not need to start growing legs and stop. A snake does not need a limb enhancer with a specific segment deleted.

Nor does it predict that the degree of decay in unused machinery should sort by relatedness, which is what the ZRS experiment found.

"Embryonic 'gill slits' are not gills"

Correct, and the older term was misleading. Human pharyngeal arches never function in respiration; they develop into jaw, middle ear bones, and throat structures.

The claim is about the developmental structures, not about breathing. The same arches, in the same order, with the same nerve and arterial supply, become gill supports in fish and become middle ear bones and laryngeal cartilage in mammals. The recurrent laryngeal nerve's detour into the chest is a direct consequence of that inherited arrangement.

The evidence is the shared plan and the constraints it imposes, not a claim that embryos breathe through their necks.

"Shared developmental genes show a common toolkit, not common ancestry"

The observation is right: Hox, Pax6, and related genes are a toolkit reused across animals.

The distribution of that toolkit is nested. Gene numbers, cluster duplications, and sequence differences group animals into the same hierarchy that anatomy and molecular data produce. A toolkit chosen by a designer would not have to fall into a tree.

It also does not address the broken components — the enhancers, tooth genes, and limb programmes retained in animals that do not use them.

What the evidence shows#

Embryos build structures their adult forms do not have, and those structures correspond to the functional adult anatomy of related groups: hind limbs in dolphins, teeth in baleen whales, limb buds in pythons.

The regulatory machinery for unused structures is often still present and can be tested directly. The snake limb enhancer still drives limb growth when placed in a mouse, at a strength that decreases as the snake lineage's limb loss deepens.

The genes that specify body axes and organs are shared across animals separated by hundreds of millions of years, to the point where a mouse gene will initiate eye development in a fly.

Haeckel's drawings were exaggerated and are not part of the modern case. Applied to human development specifically, see Atavisms and Vestigial Structures.