It’s a long time that people is fighting against the wrong use of the term “homology”. An interesting debate about the misleading use of “homology” instead of similarity occurred in 1987, originated by a Letter to Editor of Reeck et al, published on Cell [1] with several answers published on other high-impact journals (for example [2-4]). Since we were still hearing phrases like “50% homology”, “These two sequences are quite homologs” and so on, in 2008 we decided to investigate the use of the term “homology” in articles published in 1986 (one year before the debate), indexed in PubMed, and articles published in 2007 (20 years after the debate), to evaluate and compare the percentage of incorrect use of the term. The (discouraging) results of our analysis were published in a Letter to Editor on TIBS in January 2009 [5]. Since 2009 was the year of the ISMB-ECCB held in Stockholm, we decided to highlight this problem also to the bioinformatics community, and we presented to that conference this poster, that was really appreciated by the audience.
In 2010 we read an article on the Special Issue of Bioinformatics devoted to ISMB2010, in which still there was
“homology” misused in the title. Therefore, we decided to write a letter to the Editor of Bioinformatics, to point
out again this problem [6].
During this last year we still found in literature the term “homology” used in an incorrect way. Therefore, in a
further attempt to awaken people on the correct use of this term, we decided to use a different way to do it: a game.
The "Homology Game" originally consists of a poster showing six couples of objects. Five of those are couples of similar objects (some more, some less) without common ancestral origin, whereas only one couple is composed by two true “homologs”, but different, objects. The game consists in finding this pair of homologous objects. As an example of homologous objects, we chose two very different entities created by the same ancestor: Bill Gates (according to Wikipedia, Microsoft was created by BG and Paul Allen, whereas B&MGF was created by BG and his wife Melinda; therefore BG is the “common ancestor” of both entities). They are truly different in “structure and function”, but since they come from the same root, they are homologs. On the contrary, all other images we chose (lipizzan horse vs rocking horse, true comet vs crib comet, Parmigiano Reggiano vs Parmesan, baby vs doll, Italian flag vs Mexican flag) show similar objects that have no common ancestor. The choice to insert the Italian flag was made because in 2011 we are celebrating the 150 year of Italy’s foundation, and we tried to give our contribution to these celebrations with a tribute to our flag. Here the poster that we presented at ISMB-ECCB 2011, under the Section “Art&Science Exhibition”. We asked people attending the congress to play the game and put in a ballot box their answer with a motivation.
First of all, we would like to highlight that it is just a game. We had some amusing discussion about the right pair of homologous objects with players. We decided to use objects instead of real homologous organisms, first to render the game more amusing, and second to leave a more impressive message using a unusual example (as we did in our previous poster). However, our main aim was to check if people know the right meaning of the word “homology”. Therefore, we report here the results of the game, on the basis of the ballot, with a focus on motivations claimed by the players. We had 66 players. Only 15 players selected the right answer (couple “e” in our poster) giving also the correct explanation (“ancestry”). 15 more players selected a wrong couple, but their explanation proved that they are aware of the right meaning of homology, although the ancestral origin found was not correct. Overall, 18 players selected the wrong couple “c” (Parmigiano Reggiano vs Parmesan), most of them writing that “milk” was their common ancestor. This is not true, because the common origin is not determined by the raw material. Ironically, all Italian people that discussed with us the poster, excluded “a priori” the answer “c”, since Italians know very well that Parmigiano Reggiano is an original italian product, with a quality trademark and a protected designation of origin (PDO) recognized at level of international authority, while Parmesan is only an imitation, or worse, a fake. 10 players gave answer “f” (Italian flag vs Mexican flag), but 7 of them gave as motivation the fact that the two flags are similar, or have the same function, therefore proving that they were misguided by a wrong concept of homology. The other three players indicated a common origin for the two flags. However, Italian flag was created in 19th century, and it derives from French flag (the blue band was changed into green, since it is the color code for “hope”: the hope of the freedom for Italy). According to Wikipedia, Mexican flag is not derived from French flag, therefore it is not homologous, but it is very similar, to Italian flag.
From our game, it is clear that less than 50% of players showed to be aware of the real meaning of the word “homology” (also including those who named “ancestry” in their wrong answer, we totalize only 45% of players). Therefore, the problem still persists in the scientific community.
More efforts are needed to fight against this bad habit. Do you want to join to our fight? In our opinion, things to do are:
1) Please always remember to avoid the use of “homology” instead of “similarity”.
2) If you are reviewing a paper, please mark this misuse as an error to be corrected by the authors (if you want, you can cite our papers – see below).
3) If you are an Editor, please insert in the section “Instruction to authors” a statement about the correct use of the term homology.
4) If you are a teacher, say your students to avoid the use of this term in a misleading way.
A last take-home message (essentially for non-Italian people) is: beware of you when you are searching for a real guaranteed Italian parmesan product!
The letters and comments of the debate occurred in 1987:
[1] Reeck, G.R. et al. (1987) ‘Homology’ in proteins and nucleic acids: a terminology muddle and a way out of it. Cell 50, 667.
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[2] Lewin, R. (1987) When does homology mean something else? Science 237, 1570
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[3] Kimelberg, H.K. (1987) ‘Homology’ controversy. Science 238, 1217
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[4] Aboitiz, F. (1987) Nonhomologous views of a terminology muddle. Cell 51, 515–516
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Our letters:
[5] Marabotti, A. and Facchiano, A. (2009) When it comes to homology, bad habits die hard. TIBS 34, 98-99.
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[6] Marabotti, A., and Facchiano, A. (2010) The misuse of terms in scientific literature. Bioinformatics 26, 2498.
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Our posters at ISMB2009 (highlight track) and ISMB2011 (Art & Science Exhibition)