Evidence from modern biochemistry and molecular biology

The argument

Modern biochemistry and molecular biology provide deep confirmation of evolution by revealing the shared molecular machinery that unites all living things. At the most fundamental level, every known organism — bacteria, plants, fungi, animals — runs on the same basic chemistry: the same DNA and RNA storing and transmitting genetic information, the same near-universal genetic code translating that information into proteins, the same handful of amino acids assembled by the same cellular machinery, and the same core metabolic pathways powering the cell. This profound underlying unity, stretching across the entire diversity of life, is exactly what common descent from a shared ancestor predicts, and it is hard to explain on any other account. The argument deepens when biologists compare the molecules themselves across species. The proteins and gene sequences that perform the same essential functions in different organisms are not identical but differ by degrees, and the pattern of those differences tracks the branching tree of relationships drawn from anatomy and the fossil record: closely related species have nearly identical versions, distant ones differ more. This 'molecular clock' allows ancestry to be reconstructed from biochemistry alone, and it independently reproduces the same family tree. Cells are also full of features intelligible only as inherited history — the universal energy molecule ATP, conserved ancient proteins, and shared cellular structures descended from common origins. From this standpoint, the molecular evidence is among the most powerful of all, because it reaches the very chemistry of life and shows it to be unified by descent. Biochemistry and molecular biology, fields that did not exist in Darwin's time, independently confirm the relationships his theory predicted. Because modern biochemistry and molecular biology reveal the shared molecular basis of all life consistent with common descent, this argument holds, the theory of evolution is correct.

Premises

Counter-arguments

Critics from a design perspective reply that shared molecular machinery is, on their reading, equally consistent with common design — a designer reusing an optimal chemical toolkit — so biochemical unity underdetermines common descent versus common design. This is a minority objection; the scientific consensus reads the same evidence as strong support for common descent. They also note that molecular ('gene') trees sometimes conflict with each other or with morphological trees, and that horizontal gene transfer complicates a clean nested hierarchy, so the 'molecular clock' is less tidy than presented. On the mainstream view these are interpretive caveats rather than refutations: the convergence of independent molecular and morphological trees remains powerful confirmation, but the inference from unity to descent does carry assumptions the objections highlight.

Rejecting the premises

[Rejecting P1] Design critics argue shared molecular machinery is equally consistent with common design — a reused toolkit — so biochemical unity underdetermines descent versus design (a minority objection; the consensus reads it as strong evidence for descent). [Rejecting P2] Molecular gene trees sometimes conflict with each other or with morphological trees, and horizontal gene transfer complicates a clean nested hierarchy, so the 'molecular clock' is less tidy than presented. [Rejecting P3] On the mainstream view the convergence of molecular and morphological trees is powerful confirmation; the objections flag interpretive assumptions in the inference from unity to descent rather than overturning the consensus.

Further reading

https://www.nap.edu/read/6024/chapter/4