Question & Objection

Does Homology Explain the Origin of Molecular Machines?

Molecular Machines and Integrated Biological Systems
A Visit With Jesus

Proteins in molecular machines often have homologues in other systems. Shared sequences, structures, and functions provide evidence that biological components have evolutionary histories rather than appearing independently in their present forms.

Why This Matters

Homology is powerful evidence of evolutionary relationship. A design argument that ignores these relationships would fail to account for an important part of the biological evidence.

Response

Homology can establish or strongly support common ancestry and can help reconstruct the modification of components through time. It therefore contributes substantially to evolutionary explanations of molecular machinery.

But homology answers some questions more directly than others. Establishing that two components share ancestry does not by itself reconstruct the entire sequence by which an integrated system arose, nor does it alone explain the origin of the earliest member of the homologous family.

Question That Remains

Where does evidence of common ancestry provide a sufficient historical explanation, and where are additional mechanisms and intermediate stages still required?

Research Sources

Liu and Ochman — Stepwise Formation of the Bacterial Flagellar System
Renyi Liu; Howard Ochman • Proceedings of the National Academy of Sciences • 2007
Use: Gene Homology
Relevance: Uses relationships among flagellar genes to reconstruct aspects of their evolutionary history.
Source note: Sequence relationships among core genes provide evidence of duplication and common ancestry and allow a probable order of emergence to be inferred.
Pallen and Gophna — Flagella, Type III Secretion, and Evolution of Complexity
Mark J. Pallen; Uri Gophna • Genome Dynamics • 2007
Use: System Homology
Relevance: Examines homologous relationships among flagellar and secretion-system components.
Source note: These relationships provide evidence that complex molecular systems have evolutionary connections and that components have histories extending beyond their present roles.
Abby and Rocha — Evolution of Type III Secretion from the Flagellum
Sophie S. Abby; Eduardo P. C. Rocha • PLoS Genetics • 2012
Use: Phylogenetic Reconstruction
Relevance: Uses comparative genomic relationships to investigate the evolution of related bacterial molecular systems.
Source note: The study illustrates both the explanatory value of homology and the additional historical reconstruction required to move from common ancestry to a detailed account of system origin.
 The objection and response are presented separately so the reader can consider the question and the evidence for themselves.