Note to Molecular Biologists: Quit Misusing "Homology"
Homology: Similarity between species [or DNA sequences] that results from inheritance of traits from a common ancestor (Freeman and Herron 1998, Evolutionary Analysis).
Similarity: The quality or condition of being similar; resemblance. See Synonyms at likeness (The American Heritage Dictionary of the English Language, Fourth Edition).
I've been reading a lot of papers on the molecular biology and genetics of recombination and chromosomal aberrations. For those who aren't familiar with the literature, the mechanisms behind recombination and genome rearrangements (such as inversions, chromosomal translocations, and segmental deletions) are quite similar. They both begin with a double strand break (DSB) and subsequent invasion of a highly similar sequence (usually from the homologous chromosome) in order to repair that break. If the repair comes via a homologous chromosome, we get either gene conversion or a crossing over event. If, however, a non-allelic region (i.e., a similar sequence from a non-homologous region) invades, we can get a chromosomal aberration that may have biological consequences such as speciation or disease.
An overview of meiotic recombination between two homologous chromosomes, based on the DSB repair model, showing intermediates and the proteins implicated in their formation by genetic and/or molecular criteria. The points at which several proteins act is still under investigation, and some may be required at several steps. Proteins that function in both mitotic and meiotic HR are indicated in bold; all others are unique to meiosis. A DSB is introduced in a DNA duplex by the Spo11 nuclease, likely acting in conjunction with several other proteins that are known to be required for DSB induction. The 5' ends of the break undergo 5' to 3' resection to yield 3'-OH single-stranded tails. 3) One of these single-stranded tails invades a homologous duplex, displacing a D-loop. 4) Several steps resulting in the formation of a bimolecular intermediate with double Holliday junctions follow. At this point, correction of mismatches in heteroduplex DNA can result in gene conversion. 5) Resolution of the intermediate to yield a product with a parental configuration of flanking sequences (non-crossover). 6) Resolution to yield a crossover product. (http://www.infobiogen.fr/services/chromcancer/Deep/DoubleStrandBreaksID20008.html)
The molecular biologists who write articles about recombination and DSB repair usually refer to a homologous sequence being used as the template. This is usually the case, as the allele from the homologous chromosome is most common site of genetic exchange. The problem arises when they refer to degrees of homology, distinguishing between sequences of "high homology" or "very little homology" in different repair pathways. To an evolutionary biologist, this sounds like nails on a chalkboard. Homology refers to common ancestry -- two sequences are either homologous (they share a common ancestor) or they are not. There is no in between. It's kind of like being pregnant: you either are or you are not, and you cannot be "a little bit pregnant."
What these diction-deficient molecular biologists mean when they say "homology" is "sequence