Think this is really good question. From one side, homologues mean the same as relatives, so we know phrase “distant relatives” or “close relatives”.

At the same time we can’t to say(?), that all ppl have one common ancestral pra-pra-…grandma&grandpa, may be it was in different places
and in different times with different individuals, and it means that may not all the ppl are relatives. But we have common results – Homo sapiens.
From this point of view, we just have a set of properties, which define a species.
In case of proteins we have the close situation – may be on prebiotic phase of evolution in the Earth, there are a lot of places, where first protein-like
sequences were organized. So we just have a set of properties which define proteins and it means that as ancestor we just have some kind of processes.

From my point of view we can to say “distant homology proteins” if we have a strong results about a process of there divergence, otherwise
we can speculate about it only. As a measure of homology it’s possible to use a set of parameters which define a divergence process.
So the question is in the relationship of cause and effect and not in terminology.

agree with wiki : ( http://en.wikipedia.org/wiki/Homology_(biology) )

“The phrase “percent homology” is sometimes used but is incorrect. “Percent identity” or “percent similarity” should be used to quantify the similarity between the biomolecule sequences. For two naturally occurring sequences, percent identity is a factual measurement, whereas homology is a hypothesis supported by evidence.”

thanx

Just last week I rejected a paper that confused similarity with homology. That wasn’t the main reason for the rejection – there were plenty of other problems with the paper, plenty of which were confusion with terms – but it did add to it.

Zen Faulkes :

I greatly appreciate this post, as I’ve railed against the use of homology to mean “similar” many times. But might be a lost cause. We might have to live with homology having different uses in molecular biology and evolutionary biology. Having a word having two meanings is a problem, it isn’t a horrible problem. We cope with “nucleus” meaning both a eukaryotic organelle and a cluster of protons and neutrons, after all.

The two different meanings of nucleus are used in rather different context, and it is hard to imagine them being confused with each other. On the other hand, homology is used in evolutionary biology, and in molecular biology when discussing evolutionary theory, which can be confusing. Hey, percent homology has been practically eradicated (though not quite). So there’s hope yet.

Paul Gardner :

You just made me change the term “remote homologs” that I’ve used once in a paper, not in the title or abstract. I’m now using “divergent sequences” (I hope that’s better…). Phew. That could’ve been embarrassing. Now I just have to worry about the rest of the content. At least I’m not using “percent homology” anywhere.

Ha! I just updated the post to include “remote homology”. Thanks for the reminder. The PubMed dragnet nabbed 100 additional offenders, some of them good (soon to be ex) friends of mine.

The verbal shortcut is awfully easy route to take. The problem is that, in the long run, it creates more problems than it solves. A bit like the Dark Side of the Force.

Tom :
If you’re defining homology as having a common evolutionary origin, don’t a hell of a lot of things have this, if you look back far enough?
Is there little/more/lot usage, a shortcut to indicate how far they have to go back to find a common evolutionary origin for those two things being compared? (on top of other differences).

Well, if we go back far enough, all organisms are descended from LUCA, the last universal common ancestor some 2.5 Billion (American Billion: 10^9) years ago.

But the term “homology” does not apply to whole organisms, but rather to defined parts of organisms, or, in molecular biology, to proteins and genes. Let’s take wings for example: bat wings and human arms are homologous: they both diverged from the forelimb of the common ancestor of bats and humans, some 600 million years ago. But bat wings and insect wings are not homologous, even though they are both used for flying. Bat wings are adapted forelimbs, whereas insect wings are adapted exoskeletal outgrowths.

A molecular example: one of the early enzymes in the NAD synthesis pathway is L-aspartate oxidase. This is true for most animals, plants, and bacteria. However, in some bacteria and in archaea, L-aspartate oxidase does not exist in the genome, though it catalyzes a necessary step in a vital pathweay. Instead, we find L-aspartate dehydrogenase, which is completely differnt in structure and sequecne form L-aspartate oxidase, and also differnt in the biochemical functionality. But as far as physiological functionality is concerned, it serves as a non-homologous replacement to L-aspartate oxidase. Again, no homology here.

So no, not everything is descended form the same common ancestry if we look far enough. New genes and functions crop up regularly in evolutionary time.

Psi Wavefunction :
What about if you have some sort of chimaeric protein, with one domain homologous with the other protein in question while the other is not? Would those proteins still be homologous, or would partial homology actual be a sort of valid term there? Or is it best to simply specify the domain?

Since you specifically asked about a chimera, then the answer is already contained in your question. A chimera would be composed of two distinct sequences fused together artificially. So if you have protein A homologous to A’, and a chimera composed of two domains A’+B, it’s fairly tautological.

I assume though, that you were referring to natural gene fusions that happen throughout evolutionary time. The answer is the same is the chimera. The evolutionary “quantal units” so to speak are the protein domains. Just like we look for homology between organs (e.g. limbs) when we compare animals.