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If we consider homology between two nucleotide sequences as a yes/no answer to whether they have shared a common ancestral sequence, then given that all life share common ancestry and sequences are carried by living things, then how can two biological sequences be anything but homologous?

One possibility I can think of is perhaps natural transformation in bacterial---but even so, the DNA sequences picked up must have come from a biological source.

(I assume that it must be possible that there are sequences that are non-homologous, because otherwise there wouldn't be a need to point out which things are homologous, i.e. I assume that the concept of sequence homology would not be as widely used as it is right now)


There has been some discussion on my claim that homology should take a Boolean value. As I have stated in the comments, for this I refer to Inkpen, S.A. & Doolittle, W.F. J's "Molecular Phylogenetics and the Perennial Problem of Homology" in Mol Evol (2016), pp. 187.

Nevertheless, there is a general understanding that conflating the extent of similarity and the inference of common descent is always a misuse of the concept—that there can be no such thing as ‘‘percent homology.’

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    $\begingroup$ "If we consider homology between two nucleotide sequences as a yes/no answer to whether they have shared a common ancestral sequence..." But we don't. If you think we do, please cite a source that supports this idea. In fact, you are not asking a real biological question, but playing with words to expressing a philosophical opinion that is not the concern of this list. $\endgroup$ – David Oct 8 '18 at 21:15
  • $\begingroup$ I'm voting to close this question as off-topic because it is not about Biology in the terms of this list. $\endgroup$ – David Oct 8 '18 at 21:16
  • $\begingroup$ @David I refer to Inkpen, S.A. & Doolittle, W.F. J's "Molecular Phylogenetics and the Perennial Problem of Homology" in Mol Evol (2016), pp. 187. Quoting the article: "Nevertheless, there is a general understanding that conflating the extent of similarity and the inference of common descent is always a misuse of the concept—that there can be no such thing as ‘‘percent homology.’" $\endgroup$ – ning Oct 9 '18 at 3:37
  • $\begingroup$ @David I want to stress that I am not asserting my opinion. Rather, I am stating my premises which have lead to my conclusion. By doing so, I hope to expose these premises to the Q&A in addition to the actual question, to avoid an XY problem. I do not agree that I am 'playing with words'. I truly believe that there can be situations where non-homologous sequences can be created---just that I have not yet thought of them. $\endgroup$ – ning Oct 9 '18 at 3:40
  • $\begingroup$ @ning You should edit your question and insert new information there. The paper/quote for example might get buried in the comments, or later even deleted... $\endgroup$ – Arsak Oct 9 '18 at 12:48
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Homology in this context is always a matter of degree exactly because of shared ancestry. Measures of homology are often in terms of "percent homology" (or more often "percent similarity" as evidence of homology) or some other measure that allows representation of that degree.

To emphasize why this makes sense, think about a receptor family. In an extant organism, you might have 3 receptors that all are homologous. However, if receptors 2 and 3 are more similar to each other than to receptor 1, then you can make some better assumptions about the history of the evolution of receptors 1 to 3, that there is likely a "common ancestor receptor" to both 2 and 3. There is more "information" if you consider the degree of homology rather than just its existence.

At some extremes, sequences could be so different that even if they share a lineage they may have now diverged to the point that they are not distinguishable from independent sequences. However, selective pressures prevent such complete reorganization in key sequences and so at least some homology can be maintained across very distantly related organisms.

As far as deciding what is "homologous" versus "not homologous", that is somewhat of an arbitrary threshold that depends on levels of evidence and the purpose for recognizing the homology.

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    $\begingroup$ It is interesting that you argue according to degrees of homology. I was taught that homology is strictly answered in binary, or at best likelihoods, and never as a degree. A degree of similarity can estimate a likelihood (but not degree) of homology. Frankly, I do not agree with looking at homology in terms of degrees, but then your answer would not make sense unless I do. Perhaps you could elaborate on why homology should be thought of in degrees? $\endgroup$ – ning Oct 8 '18 at 19:18
  • $\begingroup$ @ning It all depends on what your goals are. I added a paragraph, does that help at all? $\endgroup$ – Bryan Krause Oct 8 '18 at 19:50
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    $\begingroup$ @BryanKrause I feel it is important to stress that degrees of homology as represented by percentage similarity is a very flawed metric, given that degrees of homology is discrete in a certain sense, determined by degrees of common ancestry. See for example Smith & Pease, 2017 $\endgroup$ – NatWH Oct 9 '18 at 7:40

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