Talk:Homology (biology)/Archive 1

Archive 1

Hands and feet

It is correct to say that human hands and feet are homologous structures? - Dominus

I think that this is a tricky one. Leaves and petals are considered homologous. While arm and leg development clearly share some processes, it is hard to say that they are homologous. Are there mutants that have arms (forelimbs) where their legs (hindlimbs) should be or vice versa? Is there any reason to believe that they were ever identical structures? AdamRetchless 02:14, 17 Mar 2004 (UTC)

I don't think they are considered homologous, as they develop from different tissues in the embryo. Yet they are clearly closely related: there's just a single developmental program encoded in the genome that's called "make a limb". This program is reused for the four limbs, with slight modifications. So hands and feet don't share ancestry, they share an instruction set. AxelBoldt 19:13, 14 Aug 2004 (UTC)

This is called "serial homology". Vertebrae of the same animal are serially homologous, for example, while your first neck vertebra is homologous to that of a mouse. David Marjanović 23:06, 5 November 2007 (UTC)

Sequence family

Is a sequence family the same as a gene family? AdamRetchless 02:14, 17 Mar 2004 (UTC)

I don't think I've ever heard the term "sequence family". However, gene family doesn't really cover everything, if we use the usual definition of "gene". For example, regulatory sequences could form a family, but wouldn't be genes. It seems not a very important distinction, though, so I'd move to have only 1 article on the topic. (Perhaps later, though, there'll be enough info to warrant one article focussing on (protein-coding) gene families in particular, and another article on sequence analysis techniques relation to, umm, sequence families.)Zashaw 03:40, 17 Mar 2004 (UTC)

( I have a question. Would brown eyes be homology eyes or blue? )

You might like to look at Sequence motif. Peak 06:56, 17 Mar 2004 (UTC)

Partial homology

Just curious about the (widely accepted) definition for genetic homology:

>In genetics, homology is used in reference to protein or DNA sequences, >meaning that the given sequences share ancestry.

How can two naturally occurring DNA sequences not share a common ancestry?

The current definition seems to imply that all naturally occurring DNA sequences that evolved from the earliest life form are homologous.

Are there some tacit assumptions about how life evolved being made? Should the definition be added to or am I missing something obvious?

Cheers

Good point. Homology for sequences should probably be defined as a matter of degree, not as a black-white issue. Some pairs of sequences are vastly more homologous than others, because the common ancestor is closer by. AxelBoldt 19:13, 14 Aug 2004 (UTC)

In a sense this is true, but in practice it really isn't. After sequences have diverged for long enough and experienced enough mutations, all visible (or theoretically observable) traces of similarity are lost. With a high enough number of changes two sequences are essentially random with respect to one another - knowing the sequence of one doesn't allow you to predict the sequence of the other.

While I may agree that homology should be a relative term, it isn't, and many people are very pedantic on this. The 'match' between two DNA or protein sequences is often reported as the similarity or percentage identity. This is the relative term. You can also talk about closely related or distantly related. However, homology is all-or-nothing. Either two sequences are (perceived to be) related by some degree (not the theoretical extremely distant relationship between all sequences) or they are not. If that doesn't persuade you then consider that if everything were homologous, the word would be useless. I think the desire is really to distinguish between similarity of function from recent divergence and similarity of function through convergent evolutionLoris

I agree with Loris--that IS the definition of homology. There is quite a bit of fuzziness in the definition of homology, but it is not so extreme that ALL stretches of DNA are homologous. If any stretch of nucleic acid were synthesized without a template, then its origins are separate from those of any other stretch of nucleic acid, so it would not be homologous. I can't think of any report that modern organisms synthesize any genetic material de novo, so this wouldn't be an issue unless we consider very primitive life, which supposedly had access to some mechanism for the de novo synthesis of amino acids.

I think that the confusion comes from the fact that "homology" includes a notion of continuity between the ancestral form and the current forms. This continuity involves traits such as function, information, structure, or selective value...but we aren't able to precisely define and identify those traits. If a sequence of DNA were determined purely by mutational forces and eventually gave rise to some functional/selectable structure (such as a gene), I would not consider the new structure to be homologous with other DNA sequences, even though they were synthesized from the same template. That's just my opinion, but I think it captures a lot of what scienstists are thinking of when they use the term "homology". AdamRetchless 01:58, 13 July 2005 (UTC)

Orthologs and Paralogs

Someone has requested an article on paralog-, orthlog- and homologous genes. Mabye you should set it up so that the searches for those additional terms are sent here (its beyond my wiki expertise), and flesh out the section a little more- a basic digaram could make it a lot more clear--nixie 04:05, 8 Oct 2004 (UTC)

I've changed the Orthlog redirect to here, to redirect to Orthologue as a fairly decent stub was already in place. --Banana04131 03:38, 22 January 2006 (UTC)

There are plenty of nice diagrams online. I found this through google (it might not be available without a subscription, but I'm sure there are others). Just search for "ortholog paralog diagram". Someone could use the basic ideas in this diagram to make something similar.

http://genomebiology.com/2001/2/8/interactions/1002/figure/F1

Does "paralog" share precisely the same meaning as homology? I ask this because the paralog page immediately redirects to homology. Shouldn't paralog have some sort of definition, linking it to homology? --Nlk

I just added a possible merge from ortholog to this article. I think the topic of homolog-ortholog-paralog can be covered in one article. Dr d12 22:41, 6 December 2006 (UTC)

I agree. Grouse 00:25, 7 December 2006 (UTC)

I added non-redundant content from ortholog and redirected it here. The first paragraph here was all about homology of structures so I gave it a section, and tried to add a more general intro to the -structure, sequence, chromosome- headings.Dr d12 04:09, 7 December 2006 (UTC)

On the use of 'binary' - jargon issues

OK, so I've just received my first revert, and since I don't agree I'd quite like to talk about it. I REALLY don't want to get into a revert war - but I will/have change it back again once. Firstly, I made several changes, so reverting the whole lot for the sake of one point seems like overkill. (Unless you disagree with those changes too of course.)
Secondly, the reason given for the revert is "explaining jargon is an important aspect of these kind of articles". This seems to me to be misguided, because it isn't relevant jargon. The article is about homology, not semantics of the word binary. The relevant sentence is either:
Homology is an all-or-nothing quality; there is no such condition as "degrees of homology."
or
Homology is a binary quality; there is no such condition as "degrees of homology."
I think using the word "binary" here is likely to be confusing to most people. In common usage at the moment it means
(a) a numbering system : base two
(b) an executable computer code file
(c) consisting of two parts
(etc).
It essentially does not mean "either completely or not at all". It may be that the term "all-or-nothing" is not recognised worldwide (it is widely used in the UK), but if not could we at least pick a better word or phrase than "binary"?

While I'm here I should point out that I also changed:
"Sequence regions that are homologous may be called conserved, consensus or canonical sequences and represent the most common choice of base or amino acid at each position."
to
"Sequence regions that are homologous may also be called conserved."
because I think the former is plain wrong. If you disagree please say so when you revert Loris 14:35, 7 March 2006 (UTC)

The use of "all-or-nothing" seems slightly colloquial, and just sounds a bit off to me for some reason. I agree that the use of binary is a bit of jargon here that we can probably avoid. How do you like my current suggestion? --Grouse 11:40, 8 March 2006 (UTC)

Circular reasoning?

"In biology, two or more structures are said to be homologous if they are alike because of shared ancestry."

Using the evolutionary definition of homology as similarity due to common ancestry is circular reasoning. How do you know that the attributes of two organisms are homologous? Because the organisms share common ancestry. How do you know that two organisms share a common ancestry? Because they have homologous features. XerKibard

You are correct in saying that it would be circular reasoning to say that two organisms share common ancestry because they share homologous features, because the use of the word homologous includes the assumption that the features have common ancestry. This is why no evolutionary biologist worth their salt would argue for common ancestry because of homologous features—common ancestry must be established before the features can properly be labeled homologous.

Did you have a suggestion for improving the article? --Grouse 12:03, 29 July 2006 (UTC)

The existence of homologous features can be seen as an independently testable prediction of basic molecular biology (ie the "central dogma"). The way history played out though, people got to see the homologous features first. From this, Darwin and others came up with the theory of evolution. I think it's the history which causes confusion, and gives the appearance of circular reasoning. Now that we understand the mechanisms, it's fair to infer common ancestry from significantly similar features, eg a high scoring BLAST hit. People tend to get lazy and sometimes say "homologous" when they should maybe say "similar". --ysnyn 27-11-2006

In other words, evolutionary homology is usually not observed directly, but only hypothesized based on strong evidence? If so, please say so in the article, preferably in the introduction. I guess developmental homology can be observed. -Pgan002 17:26, 9 February 2007 (UTC)

Creationists frequently accuse evolutionists of defining homology in a circular or tautological way. (See this TalkOrigins article.) Part of the introduction to this page also used it in a circular way, so I reworded it such that homology is used in its proper evolutionary sense. Specifically, I changed "homologous genes share a high sequence identity or similarity, supporting the hypothesis that they share a common ancestor" to "genes that share a high sequence identity or similarity support the hypothesis that they share a common ancestor and are therefore homologous." As the TalkOrigins article explains, homology is a label added after common ancestry has been established; it is not evidence for ancestry itself. To answer XerKibard's question then, common ancestry is established by any number of similar physical or genetic features (often times the same kinds of features which gave rise to the modern classification system). Once common ancestry is established, the similar features are then said to be homologous. They are homologous because of the common ancestry, not evidence for it. -Redhookesb 19:23, 13 May 2007 (UTC)

Enzymes?

Is there much difference between homology between chromosomes and genes and the homology of enzymes? In sir2 there is some discussion about the homologous nature of of enzymes between species. Rhetth

Homology means shared ancestry. Homologous chromosomes have shared ancestry. Homologous enzymes have shared ancestry. The terminology used in sir2 is somewhat confused. Grouse 00:01, 20 November 2006 (UTC)

The reason there is confusion is that homology didn't originally mean common ancestry. Looking at references before some 15 years ago will show many people talking about 60% homology, or some such number. Some people continue to use it in the original sense, mainly because it is awkward to talk about similarity of sequences when ancestry is unknown. It also gets around the problem of circular definition. Genetics411 20:35, 20 November 2006 (UTC)

"The reason there is confusion is that homology didn't originally mean common ancestry. Looking at references before some 15 years ago will show many people talking about 60% homology, or some such number." It certainly meant common ancestry even 15 years ago. While you would find claims of "60% homology" in the literature, the people making such claims are unlikely to be evolutionary biologists, and you can also find all sorts of mistakes in the literature.

Additionally there is only a problem with circular definition when the term is used incorrectly (as in claims of "60% homology"). [1]. Grouse 20:58, 20 November 2006 (UTC)

A better reference for your point is Reeck, et al., 1987 in Cell. That letter seems to have been instrumental in changing the molecular definition to match their definition. Terms do change with time, and it is not uncommon to see the same term used differently in different areas of genetics (not to mention in allied sciences, like chemistry). That Walter Fitch (a signatory) felt he had to republish the same thing 13 years after this letter does say something about the prevalence of the "wrong" definition. Genetics411 18:35, 21 November 2006 (UTC)

That is a good reference too. :) I do not think it contradicts my previous statements. Reeck and colleagues argue that the precise meaning is "having a common evolutionary origin" and that the meaning of "possessing similarity or being matched" (which they charitably refer to as the "loose meaning") has been "clogging the literature on protein and nucleic acid sequence comparisons." I think that that the the looser meaning is the new meaning. Take this quotation from the OED, "1854 WOODWARD Man. Mollusca (1856) 47 Parts which correspond in their real nature (their origin and development) are termed ‘homologous’; those which agree merely in appearance or office are said to be ‘analogous.’" While that predates evolutionary theory, the original meaning had to do with corresponding origins rather than the appearance of similarity.

I think there is a difference between a term's meaning changing within time and the incorrect use of a term. Grouse 23:06, 21 November 2006 (UTC)

I never said it contradicted your statement -- it is just a "better" reference. I don't disagree with your statement about how it seems to be used today. However, you seem to imply that the terms are, for lack of a better word, homologous. They aren't. The term homology as used by those earlier molecular geneticists is more akin to the chemical use of the word homology. It is also more similar to the derivation and use of the term "homologous chromosomes." I believe all those terms arose independently -- using, of course, the same latin root. It is not uncommon for fields to merge and have problems with terminology. To call use of homology by early molecular geneticists a "mistake" is overstating things. Genetics411 19:51, 22 November 2006 (UTC)

Orthology: confusing sentences

'The term "ortholog" was coined in 1970 to describe two similar genes in two different species that originated from a common ancestor, regardless of their function.

Homologous sequences are orthologous if they were separated by an evolutionary speciation event: if a gene exists in a species, and that species diverges into two species, then the divergent copies of this gene in the resulting species are orthologous.'

Do the two sentences above use the same or slightly different meanings of "orthology" (for "genes" versus for "sequences")? If same, why does the first one say "simlar genes", while the second says "copies of this gene"? Usually copy means exactly the same in terms of information. If different, what is the difference between "sequence" and "gene" in the second sentence? Please you introduce the term "speciation event" close to where you use it. Why do you start with the history of the term instead of its meaning? Is the term coined in 1970 still used today? Why does the section "Orthology" start by describing "ortholog" instead of "orthology"? The section should be of the form

"Orthology is ... Sequences that are orthologous to each other are called orthologs of each other. The term was coined in 1970. ..."

I cannot make the changes because I do not understand the biology. -Pgan002 20:22, 9 February 2007 (UTC)

• After my somewhat speculative copy-edits, the sentences now read as follows. Please check if this is what was intended, and please make the speciation sentence clearer. -Pgan002 22:35, 9 February 2007 (UTC)

'Orthologs, or orthologous genes, are any genes in different species, that are similar to each other and originated from a common ancestor, regardless of their functions. Thus orthologs are separated by an evolutionary speciation event: if a gene exists in a species, and that species diverges into two species, then the divergent copies of this gene in the resulting species are orthologous. The term "ortholog" was coined in 1970.'

Xenolog

i've heard the term "xenolog", what is the difference between homolog and xenolog? perhaps it should be mentioned in this article. -Martious 21:17, 23 February 2007 (UTC)

i've found a definition: Xenolog: Homolog acquired by lateral gene transfer. from [2] -Martious 21:19, 23 February 2007 (UTC)

A xenolog is a type of ortholog acquired by horizontal gene transfer. I found only one article on Pubmed that uses the term in the abstract (I just put it on Wiktionary: xenolog). Dr d12 22:21, 23 February 2007 (UTC)

Alternate ortholog definition

Being partial to the technical (actual) definition, I cut this paragraph from the article. If someone can reference the "re-definition" here is the paragraph to put back into the article Dr d12 18:21, 21 May 2007 (UTC) :

"A second definition of orthologous has arisen to describe any genes with very similar functions in different species. This differs from the original definition in that there is no statement about evolutionary relation, or similarity in sequence or structure. This expanded use of orthologous is often criticized for confusing the meaning of the word, and furthermore being theoretically unsound, as the idea of a "very similar function" requires arbitrary cutoffs for similarity, and it is not clear how similarity of function is to be measured in different organisms."

References

I have tagged this article because it reads like one long POV OR essay that fails to give citations throughout for the statements it makes. It needs to have many more citations from reliable sources to improve it. This is not to say it is factually inaccurate, merely that it needs greater reference support. Peter morrell 07:22, 3 November 2007 (UTC)

Metalogues

A orthologue of a paralogue is called a metalog, metalogues are an issue because if you swap an metalogue for an orthologue, your data will tell you the age of the gene duplication (creating paralogues) and not of the speciation event (make an orthologue of each paralogue). COG is a solution. I do not know how to refernce that without doing some research and most importantly it is tongue twister and I am not a great writer (is anyone in science?!). Cheers --Squidonius (talk) 17:46, 22 November 2007 (UTC) PS a funny note: Is the UK/US spelling switch here done purposefully? It shows who wrote what, it is great!

Improving the Picture

Color-coding the homologous bones in the picture that compares forelimbs would help immensely, lending it immediate visual clarity of what the picture is intended to illustrate. Presently the meaning is not immediately obvious to the casual viewer. CarpeScientia (talk) 14:48, 22 February 2008 (UTC)

It would also help to change the captions in the image to be in English rather than German. I know that there is a translation, but its not immediatly obvious that it's there since it's half way down the page. Perhaps just moving the translation to somewhere more obvious would help. --AngryBacon (talk) 17:41, 26 March 2008 (UTC)

"Six flood arguments" article

Except that the article is flawed, I do not understand how it relates to the subject: http://www.lhup.edu/~dsimanek/6flood.htm —Preceding unsigned comment added by 41.15.167.247 (talk) 17:19, 25 July 2009 (UTC)

Platypus

Are the venom glands of the Platypus related to the anal glands possessed by some other mammals, or are they a different development? Drutt (talk) 17:18, 16 November 2009 (UTC)

Available classification of homology related concepts

We have published an ontology_(information_science) of homology-related concepts. The ontology and the definitions within it are free. The community is welcome to re-use whatever information you might find useful.

[3] The ontology (free access and reuse)

[4] The paper (not free access) (but there is a free preprint of the paper on my homepage)

Marcrr (talk) 10:44, 17 March 2010 (UTC)

homology also has a very practical application in research

In the opening section, the article goes "Homologous[Etymology 1] traits of organisms are due to sharing a common ancestor," This is the only use that is mentioned in the article by a fast overview. In practical molecular biological research, homology has a very practical application. A researcher will look at the homology with other correspondent genes, and decide that regions of highest homology are often the places to start looking for interesting stuff like catalytic site, regulatory site etc. Regulatory regions in the DNA also tend to have well conserved DNA sequences. Even though I cannot at the moment state a specific article to back up my claim, I know that this is a common practice, and so should deserve mention in this article. Maybe as a "practical uses of homology" or something. —Preceding unsigned comment added by 90.184.37.117 (talk) 09:45, 26 March 2011 (UTC)

Homologies across phyla

Discussions of homology commonly limit themselves to the limbs of tetrapod vertebrates, occasionally touching on other structures, such as modified teeth as in whales and elephants. When you try to cross phylum boundaries, even among apparently related phyla such as among the protostomes within bilateria, things become murky. For instance, can we even say that the mouth or eyes of a spider are homologous to the mouth or eyes of a gastropod? Even within phyla, there is need for concrete and referenced statements which structures (for instance the various mouth parts of spiders vs. insects) are, or are not, homologous, or that it would be meaningless to say. Would it be meaningful to specify which pairs of legs are present or lost in insects relative to arachnids relative to decapod crustacea relative to centipedes? And then there are plants; leaves--tendrils--some (but not all) spines, etc. I may put a section in the article to generalize the concept, but I feel a specialist might do it better.Martino3 (talk) 15:43, 28 March 2011 (UTC)

It's a complicated issue, but the highly limited understanding I have of the topic leads me to suspect you'll find Gunter Wagner's work (most of his papers are on his website) pretty illuminating. Part of the issue is homologous genes vs structures vs mechanisms - if an ancestor has legs, and one of its many descendants alters how the leg is built by using different signal pathways or genes, is it still homologous? I'd argue yes, especially because even within tetrapod limbs, you see a lot of variation in underlying mechanisms and even genes present. Alternatively, consider your eye example - if the common ancestor simply had a patch of photoreceptors, in one sense, both eyes evolved from the same source, but in another, they represent independent convergences on lens-based image-forming eyes.

Anyhow, the key is to avoid WP:OR - if you can find papers discussing this issue (and I suspect there's plenty), cite away, but we shouldn't be synthesizing information or drawing our own conclusions or points here. Mokele (talk) 17:00, 28 March 2011 (UTC)

In-Paralogs, Within Species Out-paralogs, Between Species Out-Paralogs

I believe the distinction between In-Paralogs, Within Species Out-paralogs, Between Species Out-Paralogs should be mentioned in the ortholog/paralog section as specified in the Koonin 2005 paper. Dopeytaylor (talk) 17:21, 21 June 2011 (UTC)

Analagous Traits

I slightly modified the second paragraph where a reference is made to analogous traits. In one sentence it is stated that analogous traits might share a common ancestor, then in the next it is stated they might share a common ancestor. I believe these two statements are contradictory,Dopeytaylor (talk) 14:33, 18 August 2011 (UTC)

In / Out paralogs definition

This is from the article. I think this should read "happened before speciation". Can someone who knows this stuff please comment?

Paralogs can be split into in-paralogs (paralogous pairs that arose after a speciation event) and out-paralogs (paralogous pairs that arose before a speciation event). Between species out-paralogs are pairs of paralogs that exist between two organisms due to duplication before speciation, whereas within species out-paralogs are pairs of paralogs that exist in the same organism, but whose duplication event happened after speciation.

My rationale: if an in-paralog is a paralogous pair that arose after speciation, and a between-species out-paralog is a paralogous pair between two organisms whose duplication event happened before speciation, then I would expect a within-species out-paralog to be a paralogous pair that exists in one organism and whose duplication event also happened before speciation. If it is "after" and not "before", then the within-species out-paralog definition overlaps the in-paralog one and there's no definition covering the missing "before" case, which doesn't makes sense. --Saforrest (talk) 12:48, 25 September 2012 (UTC)

I'm not sure what you are asking for. Between-species in-paralogs do not exist. In-paralogs must be in the same species. Out paralogs can either be within, or between species. Can you be more clear about what you are arguing for?Dopeytaylor (talk) 20:27, 16 September 2013 (UTC)

Paralogy Regions

It has been suggested to merge the article 'Paralogy Regions' into Homology in the Paralogy section. Well, yes, it could go into Homology but I feel it should not merge directly INTO paralogy, since paralogy regions are a very special case of paralogy. There is plenty of paralogy exisitng in genomes (eg. from tandem gene duplication) that is not part of any paralogy region. So, if merging into homology, a new section should be made for 'Paralogy regions', just below 'Paralogy' Euglossa (talk) 22:06, 9 December 2012 (UTC)

I agree to merge paralogy regions into paralogy. I don't see a big difference between paralogy and paralogy regions" - it's just a matter of size and quantity. However, a figure would be helpful to illustrate the two and how they differ. Peteruetz (talk) 16:18, 7 September 2013 (UTC)

I think this can be facilitated by simply being more general in the definition of paralogy. DNA that arose due to genome-internal duplication is a paralogous region. If there are genes involved then they are paralogous.Dopeytaylor (talk) 20:27, 16 September 2013 (UTC)

Proposal to split the article into ″Homology (evolutionary biology)″ and ″Homology (sexual differentiation)″

There is an attempt, in the section Anatomical homology, to treat these two senses on the same footing, as particular instances of a general concept. However, this is unreferenced; moreover, I did try to find sources to support treatment along those lines, but have not been able to find any. Indeed, everything I was able to find was clearly one thing or the other, with no conceptual relation between the two mentioned anywhere.

Unless someone can dig up an appropriate reliable source, I would think that the present article should become a disambiguation page, with links to the two new pages. Reuqr (talk) 02:46, 3 September 2013 (UTC)

Two things: First, I don't think "sexual differentiation" is the best term - "developmental homology" might be better. But this leads into the bigger, second issue, which is that these *are* all related by the central question of the developmental origin of a structure. A bat's wing and a human arm are not only evolutionarily homologous, but are developmentally homologous too. That such homology occurs below the species level (as in between the sexes) is merely a special case of a more generalized theme of different structures originating (whether over developmental or evolutionary time) from the same precursors and sharing some of the same developmental pathways, just diverging from the other form's pathway at a later or earlier point. Unfortunately, I'm not really familiar with the evo-devo literature enough to have citations; this is just what I've picked up from various books, courses, seminars, and symposia over the years. HCA (talk) 14:07, 3 September 2013 (UTC)

Namewise, I was unsure myself whether it should be "developmental″ or ″sexual differentiation,″ before opting for the latter... but this is something we can talk about later (and, I think, we should talk about it, regardless of whether we decide to split the page or not—I think it should have a proper name regardless of whether it has a separate page).

Page-splitting-wise: clearly these is some conceptual relation between (excuse the labels) the ″evo-homology″ and ″devo-sex-diff-homology,″ but the issue is 1. is this relation really so strong that the two are best viewed as two sides of the same coin (two instances of the same general thing, or some such statement), and 2. can we find reputable sources to confirm this. Even if the idea is ″in the air,″ we should have some sort of reference (so, HCA, if the names of some of those seminars, books, etc. that you mentioned above (or just the names of their authors) should come back to you at some point...)

As it happens, I just found out that Wagner (in ″The Biological Homology Concept,″ currently Ref. 3 in the article) does attempt to treat the two concepts on the same footing. I'll quote him, from p. 62, for reference:

Based on the attempts to find and express the biological homology concept reviewed above, a preliminary definition of biological homology is discussed in this section.

DEFINITION Structures from two individuals or from the same individual are homologous if they share a set of developmental constraints, caused by locally acting self-regulatory mechanisms of organ differentiation. These structures are thus developmentally individualized parts of the phenotype.

This definition is both more inclusive and more restrictive than the historical homology concept. It is more inclusive because it allows homology between parts of the same organism, i.e. iterative homology, and between individuals of the same species. The latter (between two individuals) is important to include for homology between sexually differentiated parts (e.g. penis and clitoris, or testis and ovary), or between different generations in a complex life cycle (e.g. parthenogenetic and sexual generations of parasitic insects).

Note, however, two things: 1. this is a proposal of a novel definition, which, it seems to me (from having superficially browsed a not-so-great corpus of literature), has not been widely accepted since the paper got published in 1989; 2. he explicitly says that his definition is more inclusive than the historical one in part because it allows for homology between individuals of the same species, in particular for homology between sexually differentiated parts. Thus it would seem that the traditional definition would not consider the latter as falling within its province. (For future reference, when we start discussing the name: note that he uses the keyword ″sexually differentiated″ here.)

I'll continue looking, but so far in my literature search, this is a lonely example of trying to bring the ″evo-homology″ and the ″devo-sex-diff-homology″ within the same conceptual framework. At this point, I would still vote for splitting, with a mention, on each of the two new pages, that there have been attempts (cite Wagner, and hopefully some others) to treat the two concepts in a unified way.

Another thought: from the standpoint of medicine, the ″devo-sex-diff-homology″ is, arguably, all that matters; if one principally cares about medicine, why burden him or her right off the bat with all the links to evolution and moreover all the definitional difficulties that the more general concept of homology comes with—especially since the definition of the more narrow, medically relevant term seems to be entirely controversy free? The point being: this relevance to medicine is, I think, reason enough for ″devo-sex-diff-homology″ to have its own page. Reuqr (talk) 03:27, 4 September 2013 (UTC)

I'd actually consider the Wagner ref a huge vote for keeping - he's a Big Name in the field (big enough that those outside it, like me, have heard of him and his work). And when you plug "Biological Homology Concept" into Google scholar, it turns up several hundred papers, and the article itself has been cited over 250 times, which is pretty impressive given how tiny the field of evo-devo is. I vaguely recall that Sean Carroll's work contains similar concepts, though I've only read a little of it. Additionally, from a scientific perspective, I actually think Wagner is correct in this, and that the concepts should indeed be unified.

As for medicine, I'd say both are useful, and back when I was TAing med school anatomy, we used evolutionary homology extensively to explain *why* certain structures were arranged the way they are (and why defects in one correspond to defects elsewhere). Pretty much nothing in the skull and neck makes any sense unless you're familiar with shark anatomy, for example. The anatomy of the heart and its major vessels is entirely due to ancestral gill-arch vasculature patterns that have been altered. The urinary and reproductive ducts depend upon our 3 pairs of kidneys, only the last pair of which are retained in amniotes. Without knowing these, you're just memorizing by rote repetition. HCA (talk) 16:13, 4 September 2013 (UTC)

I am neutral on the subject. Either way, I think the introduction and definition section need to be broadened in order to accommodate the sexual-dimorphism view of homology. If they are split, then this broader definition can be used on a redirect page that briefly outlines homology in each context, then provides a link to a more extensive page. You could almost place sequence based homology on its own page as well. Given the extent of that section it might be a good idea (although some streamlining definitely needs to be performed).Dopeytaylor (talk) 12:21, 17 September 2013 (UTC)

With regard to the proposed split: Per WP:Content fork, we should strive to keep aspects of a topic in one article instead of causing readers to go to multiple articles, unless necessary. I don't see any reason to split in this case, given that all the definitions/concepts have to do with biology. No need to confuse readers further than they might be from trying to understand the different definitions.

Specifically regarding the definitions, I feel that Reuqr's version of the lead was somewhat less helpful than the lead previously was. I was aware of Reuqr's changes, meaning this, this and this edit (which Sowlos fixed/tweaked a bit here and here), but I decided that I would comment on this matter at a later date (which is why I'm here now). The problem that I had with Reuqr's version of the lead, other than it having been too big (per WP:LEAD), was that it did not explain what the term means right off the bat. Per the WP:MOSBEGIN guideline (especially the "First sentence" part of it), we should not start off the lead stating "The term homology has several related meanings in the life sciences." Reuqr's first change to the lead at least had the wording "with the underlying idea that two different characteristics, in two different biological entities, display homology (or, are homologous) if they 'develop' from the same structure or organ." But his finished product didn't have that in the first sentence. The article should use the most common definition first, or include one of the definitions first, unless the topic does not have a most common definition or is too difficult to define in one sentence. Defining homology isn't a "too difficult" case, in my opinion. And keep in mind that a lot of our readers, maybe the significant majority of them, come to this article to find out what homology, homologue or homologous mean. The lead was also less encyclopedic, considering that it referred to itself (WP:Self reference) and was partly in bullet-point format.

JSquish's edit, and Dopeytaylor's edits ([5][6][7][8][9]), to the lead have made the lead much better, though I do wonder if the sexual differentiation aspect should be mentioned first (as it previously was), given that perhaps most articles that link to this article are referring to that definition; I haven't yet checked. I did, however, re-bold the lead, per WP:MOSBOLD. Something else to think about is that, these days on Wikipedia, "refers to" and "defined as" have been getting removed from the first sentence of the lead, per the WP:REFERS essay. Dopeytaylor's use of "simply defines" for the first sentence might be an exception, though. Flyer22 (talk) 02:04, 18 September 2013 (UTC)

Thank you for the comments Flyer22. I placed the sexual differentiation definition last because this definition is secondary to the evolutionary definition. Within the evolutionary definition I would even argue that the sequence version predominates within the sciences. I believe others would back me up in this assertion, but think it is out of the scope of this thread. We can certainly debate this issue, and I think it should be vetted in the proper way.Dopeytaylor (talk) 14:45, 18 September 2013 (UTC)

I see, and think that you are very likely right about that definitional aspect. Flyer22 (talk) 15:05, 18 September 2013 (UTC)

I agree about the sexual differentiation being secondary, but I don't think the sequence version is predominant - the anatomical definition is definitely the most common in fields that operate at biological levels above molecular, and is the original definition (since, after all, we've only been sequencing for about 50 years). HCA (talk) 15:21, 18 September 2013 (UTC)

This is fine. Shall the merger move ahead then?Dopeytaylor (talk) 18:53, 18 September 2013 (UTC)

The reason I abandoned the attempt to provide a unifying definition of the evolutionary and sexual-differentiation homologies in the lead ("with the underlying idea that two different characteristics, in two different biological entities, display homology...″) was that I realized I was doing OR. When I tried to find references, I saw that the proportion of those that try to provide some kind of unified picture is simply microscopic, and moreover, even in that tiny group, there is no ″consensus″ account to be found in multiple sources. Now, HCA assures me that it is well-accepted in the field that there is a unifying concept, and I have no reason to doubt that assessment; but even so, from what I've seen so far, this is simply not reflected in the published literature. Thus I feel that presenting these two concepts from a unified point of view misrepresents the situation as it actually exists in the field; 99.99% of the time, the two concepts of homology are not discussed together.

And yes, they both have to do with biology, but at this point, they are just homonyms with only a potential to become unified. And homonyms, I think, should be disambiguated. An example from physics: the word ″adiabatic″ has two quite different meanings, reflected, as they should be, in two different articles (Adiabatic process and Adiabatic theorem; look at them---they certainly seem to be very different). And yet, there actually is a deep connection between the two (see e.g. here for an attempt to elucidate it). Nevertheless, 99.99% of time, the two concepts don't mix, and they accordingly have separate articles, despite the fact that they are both about physics. Of course I realize that the preceding example does not have the power of a precedent, nor should it; I'm just trying to explain why I think a split would be the right thing to do.

As far as how the lead is written, and what should and should not be in the first sentence: I don't think one can do a proper job in the first sentence, precisely because the two concepts of homology are so different. So the lead will either violate the ″first sentence″ guideline, as mine did, or else define just one of the concepts, and then, from the perspective of an uninitiated reader, quite surprisingly introduce the other concept that, true, has the same name as the first concept, and, true, has to do with biology, but otherwise, for all that the reader has learned up to that point, has nothing else in common with the first concept. One has to pick one's poison, and it is a matter of taste which one to choose. The only way to avoid poison-picking is to split the article---UNLESS someone can show that the above analysis of the state of the matter in the literature is wrong, in which case the first sentence can be the unified definition, followed by particular instances of it in the evolutionary and sexual-differentiation contexts. Reuqr (talk) 02:05, 21 September 2013 (UTC)

Just focusing on your last paragraph about the lead, I generally disagree. On Wikipedia, we often begin the lead with one definition and then branch into other definitions of the term and/or concept; the most common and/or most authoritative definition is usually put first. That is standard practice. Dopeytaylor has worded the lead so that it is clear that the first definition is defining homology in general terms as "a relationship between a pair of structures, or genes, due to having shared ancestry." It continues on from there, first describing the evolution aspect; the lead describes that first, over the sexual differentiation aspect, per WP:Due weight. It then describes the sexual differentiation aspect. Dictionary definitions and encyclopedia definitions begin a topic with one definition and then branch into the other definitions. They don't give a vague definition right off the bat, and they don't stack all the definitions into one long run-on sentence; neither should we do that on Wikipedia. Like I stated, an exception to starting off with a vague definition is if the topic is too difficult to define in one sentence, like defining the Universe is. I don't believe that is the case with this topic. Furthermore, even when defining the lead is not about putting the most common definition first, Wikipedia still often starts out with one definition and then branches into the others; take a look at the WP:Featured article Atheism for an example of how to present definitions of a topic in the lead.

As for splitting the article, I disagree, per the reasons I've already stated above. I don't consider your proposal as a valid example of when a split should happen. Flyer22 (talk) 02:31, 21 September 2013 (UTC)

All of what you're saying is, indeed, standard and unobjectionable provided the two definitions are truly related. My main point, which no one except HCA has really addressed, is that in the published literature, there is very, very little support for the claim that the two really are related as opposed to being mere homonyms; in fact, so far, I know of maybe two or three papers that do it. And even if I was able to find ten, consider this example: in Gilbert's Developmental Biology, 7th ed., the word stem ″homolog″ appears 150 times. All of them refer to either evolutionary homology or to homologous chromosomes. The section on sex determination would have been a nice opportunity to talk about sex-diff-homology---and the author does not take it. The few papers that do treat the evo- and sex-diff-homology together are strictly theoretical biology, in fact bordering on philosophy of biology, and are thus not representative.

The fact that both of the homology concepts have to do with biology is, I think, simply not enough, es evidenced by the fact that homologous chromosomes have their own page. By your logic, you should support merging that page with this one (should anyone suggest it). But would you really?

So my argument, in a nutshell, is this: if the two homology concepts are mere homonyms, then I would think it obvious that they should have separate pages. Literature (as best as I can tell) does not really support the view that they are more than homonyms. And thus my proposal for the split. And I am wondering if those who are against the split could explain where in the published literature do they find strong (or even moderate) evidence for the claim that the two concepts are not mere homonyms. Reuqr (talk) 14:17, 21 September 2013 (UTC)

Regarding this comment you just made (now seen above), there are factors that go into an article being a standalone article and when an article should be split. I don't know what to state to make it even clearer to you why I believe that this article should not be split in the way that you have proposed. Dictionaries and encyclopedias don't have a problem covering the topic of homology with regard to biology (where both evolution and sexual differentiation are usually mentioned) in one entry, and I don't see why Wikipedia, as another encyclopedia, should have that problem either. Flyer22 (talk) 15:08, 21 September 2013 (UTC)

Look, this whole debate will become a non-issue (as far as I'm concerned, anyway) as soon as someone provides evidence that the concepts are treated as two aspects of the same thing in the literature. You say that encyclopedias and dictionaries have no problem defining both concepts under a single heading? Well, which ones? Not Britannica online ( http://www.britannica.com/EBchecked/topic/270557/homology ); not Merriam-Webster ( http://www.merriam-webster.com/dictionary/homology ); and not Oxford English Dictionary ( http://www.oed.com/view/Entry/88078#eid1511374 ). Take a look at them: not one of these three fairly heavy lifters includes anything that can fairly be described as a paraphrase of ″male and female organs are homologous if they develop from the same embryonic tissue.″

As far as how to make it ″any clearer″ which pages should be split and which ones shouldn't, you could explain why you think (if you think) that the page on homologous chromosomes should remain separate from the present page. Remember, your explanation for why evo-homology and sex-diff-homology should be kept together is because 1. they are both called ″homology″, and 2. they both have to do with biology. Well, by that standard, homologous chromosomes should be on the same page, shouldn't they? By the way, so far, the case for the merger of the chromosome-homology concept with evo-homology is stronger than the case for keeping the sex-diff-homolgy, because at least the OED entry mentions the chromosome-homology, but not the sex-diff-homolgy... — Preceding unsigned comment added by Reuqr (talk • contribs) 17:50, 21 September 2013 (UTC)

I did look at the Encyclopædia Britannica source before commenting to you in my "02:31, 21 September 2013 (UTC)" reply, and its first line is consistent with Dopeytaylor's first line of the lead that states "a relationship between a pair of structures, or genes, due to having shared ancestry." I don't take the Encyclopædia Britannica's first line as necessarily excluding sexual differentiation. That entry focuses on the evolution aspect, but, as noted above, more weight is often given to the evolution aspect in sources and there's also the fact the entry is titled homology (evolution). As for Merriam-Webster, it is obviously covering the sexual differentiation aspect of homology in addition to the evolution aspect, just like the significant majority of (if not all) dictionary sources do, though it is not explicit on the fact that it is covering sexual differentiation. I do not have access to the Oxford English Dictionary source. And let's keep in mind that the matter can also be searched under the terms homologue and homologous. Yes, judging by the relatively small size of the Homologous chromosome article, there would be no problem merging it with this article. Per WP:Content fork and WP:Split, it can be split when it needs to be. That stated, it is specifically about homologous chromosomes. Your argument that my argument means that the Homologous chromosome article should be merged here is essentially stating that we should not have separate articles for aspects of a topic. We do that when it is sufficiently reasonable, per WP:Content fork. I do not find your proposal of a split sufficiently reasonable (for reasons I've already gone over above). I stand by what I've stated to you above on this matter. Best to see what others have to state on it and/or start some form of WP:Dispute resolution on the matter. Flyer22 (talk) 18:31, 21 September 2013 (UTC)

Let's not do any dispute resolutions just yet... (or ever, if I can help it). There's no rush, after all; it's not like there's an edit war in progress. Let's wait and see if anyone else wants to chime in. But in the meantime...

As far as OED, here you go: OED: homologous; OED: homologue; and OED: homology.

You keep saying that you don't find my split proposal sufficiently reasonable, ″for reasons [you've] already gone over above.″ Well, I just reread everything you've written in this thread so far, and here are the reasons you gave:

1. Per WP:Content fork, we should strive to keep aspects of a topic in one article instead of causing readers to go to multiple articles, unless necessary. I don't see any reason to split in this case, given that all the definitions/concepts have to do with biology;

2. Dictionaries and encyclopedias don't have a problem covering the topic of homology with regard to biology (where both evolution and sexual differentiation are usually mentioned) in one entry.

(If I missed a reason, my apologies; please point it out to me.) Now:

As far as reason #1, if it rests on anything, it rests on some sort of general principle. That general principle seems to be, ″if a concept is called homology, and has to do with biology, then it should be on the same page with all other biologically-related homology concepts." Thus my counter-example of homology between chromosomes. You still didn't explicitly state, by the way, if you actually think that chromosome-homology belongs in the same article with evo-homology or not; all you said is that size would not prevent a merger. But do you actually think they should be merged? If yes, the reason is the principle I just outlined, and you are, well, at least being principled (though probably going against prevailing opinion); and if no, then you need to explain why the principle does not apply there.

And as far as reason #2: I take it you don't actually have examples of dictionaries and encyclopedias where ″both evolution and sexual differentiation are usually mentioned″? What you do have is: "Not necessarily excluding"? "Obviously covering...though it is not explicit on the fact that it is covering sexual differentiation"? (How is it obvious then, one might ask?) Surely, what we need is a source of that caliber to be explicitly including, not merely not explicitly excluding? Put another way: even if I grant that these sources might be consistent with including sex-diff-homology, they are even more obviously consistent with explicitly excluding it!

And I gave that Britannica article because there is no article in Britannica dedicated to sex-diff-homology at all---you can search for the entry ″homology″ and see for yourself.

Again, it is very simple to convert me: just produce some sources of the caliber of Britannica, OED, and Merriam-Webster that indeed explicitly mention both evo- and sex-diff-homologies under the same heading (provided that heading does not also include the non-biological meanings, of course!). After all, you say that ″significant majority of (if not all) dictionary sources do.″ If you can find some, I'll take a look at them and we'll take it from there. Reuqr (talk) 21:18, 21 September 2013 (UTC)

I think Reuqr has it right. This proposal is taking the wrong approach. The issue of whether evolutionary and sexual homology should have their own articles is irrelevant to whether homology as a whole deserves its own article. It is the Wikipedia way to group relevant content together into single articles while creating sub-articles for the more focused facets of each topic.
In my opinion, biological homology, as a whole, should have its own overview article and (if we have enough source material) its variants can have sub-articles spun off. Sub-articles would probably result in a smaller article here, but that would also mean content which has a hard time meshing in a single article can be segregated from each other. Let's not throw out the baby with the bath water. —Sowlos  22:12, 21 September 2013 (UTC)

Hmmm... this sounds more like you think that I don't have it right. After all, you are saying that this present article should definitely stay, and the subarticles should appear only if we have enough source materials. My point of view is precisely the opposite: I think there is definitely enough source material for an evo-homolgy article, and enough source material for sex-diff-homology one; what I have trouble finding is material that could justify an article that, like the present one, treats these two homology concepts as two instances of the same thing. Remember, I had originally actually tried to provide a unifying definition in the lead. But then I gave up, precisely because I could not find enough support in the literature, and what I was writing was turning into original research. Reuqr (talk) 22:56, 21 September 2013 (UTC)

Reuqr, there are dictionaries, found from Googling or going to a local library, that either explicitly or non-explicitly include sexual differentiation in the definition of homology. You are asserting that dictionaries don't include it, that the evolution aspect is the only aspect found in dictionaries? This The Free Dictionary source, for example, shows various dictionary definitions of homology that obviously cover sexual differentiation. And of course the definition of homology includes sexual differentiation in general, such as in this, this and this source found on Google Books. That third source (page 10) treats both concepts together stating, "A similar structure found in two or more organisms may have formed either from the same embryonic tissues in each organism or from different embryonic tissues. A structure that arises from the same embryonic tissues in two or more organisms sharing a common ancestor is said to be homologous." There are various WP:Reliable sources like that on Google Books and elsewhere, and a good number of them are not referring to the sexual differentiation aspect as "homologous chromosomes." But there are also sources like this one and this struggling to provide a biological definition of homology, with the latter stating that the concept has often been confused with other matters (such as analogy, homogeny and homoplasty). Both sources contrast my view that "homology" (with regard to biology) is not a matter that is too difficult to define. As for the Merriam-Webster definition, the first definition states "a similarity often attributable to common origin." That is the main example I mean by stating that it covers sexual differentiation without specifically stating "sexual differentiation." Many other dictionaries are like that, clearly covering sexual differentiation without specifically stating "sexual differentiation." It's a general definition applying to both the evolution and sexual differentiation aspects. I'm sure that you can see how that wording applies to sexual differentiation; if you can't, I don't know what else to state to you about that. Either way, I have stated enough on this matter and am, at this time, done replying to you on the topic. Of course...I may feel inclined to reply later, especially if this matter goes to some form of dispute resolution.

Sowlos, since Homology is a disambiguation page, I take it that you are referring to Homology (biology)? You feel that it should remain as an overview on homology in biology? If so, I agree with that...but not with the aforementioned split. Flyer22 (talk) 23:00, 21 September 2013 (UTC)

Yes, I was referring to Homology (biology) and suggesting it remain as a single overview. I disagree with the proposed split. —Sowlos  12:11, 22 September 2013 (UTC)

I respect Flyer22's decision to disengage from the argument with me, at least for the time being. That is certainly his or her prerogative. But I also hope that it is obvious that this will not prevent me from countering those points in his or her last post that I think need to be countered.

I think I finally see what Flyer22 is trying to say with regard to sources such as Merriam-Webster... but, alas, this does not bring me any closer to agreement.

First of all, Flyer22 was initially claiming that "[d]ictionaries and encyclopedias don't have a problem covering the topic of homology with regard to biology (where both evolution and sexual differentiation are usually mentioned) in one entry". I hope we can all now agree that none of the dictionaries and encyclopedias either one of us looked at thus far mention—and surely the word "mention" is to be taken literally here!—sex-diff-homology under the same entry as evo-homology. (In fact, even in his or her latest post, Flyer22 repeated that "there are dictionaries... that either explicitly [emphasis mine] or non-explicitly include sexual differentiation in the definition of homology." I hope we can at least agree that none of them mention it explicitly after all.)

Thus, Flyer22's has modified his or her claim (I'm not suggesting there's anything wrong with modifying the claim, by the way; reasoned arguments are fluid things)—namely, Flyer22 now says that what there is in Merriam-Webster etc. is sufficient for his or her purposes, even if it does not mention sex-diff-homology explicitly. Here is what I think about that.

I don't deny that if someone used the phrase ""a similarity often attributable to common origin" (the meaning #1. in Merriam-Webster's "homology" entry) when describing sex-diff-homology, that this someone would be saying something true. Rather, I deny that such a general, non-technical statement is sufficient grounds for claiming that the technical concept of evo-homology and the technical concept of sex-diff-homology are but aspects of an overarching technical concept called ″biological homology.″ (And, yes, I claim that there needs to be such an overarching technical concept if the two subconcepts are to be treated on the same Wikipedia page; for otherwise, we have a single page that treats mere homonyms.) I think that the support for the overarching technical concept should also be technical, rather than vague and general. If an argument for this last statement is required, consider that the Merriam-Webster's meaning #1. could arguably apply to homologous chromosomes as well, but (as I keep pointing out), no one thinks that that article should be merged with the present one. Thus the wording in 1. is just too vague, broad, and, well, non-technical, to be of any help.

On another track, Flyer22 provided other (i.e. non-dictionary and non-encyclopedia) sources that, he says, mention sex-diff-homology explicitly. (I hope it is understood that what is, or should be, meant by this is: explicitly mention both evo-homology and sex-diff-homology as particular cases of an overarching general technical concept of homology; for a genuine example of such a mentioning, see the passage from Wagner I cite near the beginning of this thread.) None of the sources provided by him or her mention both evo-homology and sex-diff-homology explicitly, or could be fairly read as implying that they mean to subsume both in their discussion. The only reason I can see that would lead Flyer22 to assert different is that the sources mention the phrase "same embryonic tissue." But that's not enough! In this source, the topic is evolution; evo-devo being as important as it is, of course there will be talk about the "same embryonic tissue" at some point, even if (as is the case in 99.99% of articles on evo-homology) there is no intention to talk about sex-diff-homology at all. Again, in an article about evo-homology, what is required is an appearance of something that can be fairly interpreted as a paraphrase of this: "male and female organs are homologous if they develop from the same embryonic tissue." In the second source, on the other hand, sex-diff-homology is clearly there—but evo-homology is not mentioned at all. And finally, consider the third source, the one Flyer22 emphasized. Page 10 of that source is manifestly not about sexual differentiation! The phrase "sharing a common ancestor" is very non-ambiguous in that respect, and the one thing that is obvious about that page is that it is about evolution, and only about evolution: it talks about forelimbs of amphibians and mammals, and never mentions anything like ovaries and testes or any other paradigmatic examples of sex-diff-homology. Surely, if the intent of the author was to subsume sex-diff-homology in the discussion, these paradigmatic examples would have made an appearance.

Incidentally, I don't deny that there are some sources that do mention sex-diff-homology and evo-homology in the requisite way—I provided an example of one myself! (That's the passage from Wagner, near the beginning of the thread.) But the problem is that such articles are highly atypical of both evo-homology literature and sex-diff-homology literature, or at least so it seems evident to me, having done some research into the matter. And this is why dictionaries and encyclopedias could be helpful here: if they did mention both homology concepts as aspects of an overarching technical "biological homology" concept, that would be enough to justify treating both concepts on the same Wikipedia page. But so far we have been unable able to find any dictionaries or encyclopedias that treat the two concepts in the requisite way.

(I can't reply to Flyer22's sentence that ends with " a good number of them are not referring to the sexual differentiation aspect as 'homologous chromosomes'," because I don't understand what he's trying to convey there.) Reuqr (talk) 10:32, 22 September 2013 (UTC)

I am female, and I mostly don't understand what you are trying to state or your logic on this matter. It is logic that I have seen few others make on this topic, and none quite like yours. And your "let's split the article" argument is not sufficient for reasons I've noted above. You have misrepresented my comments/motives above, especially in your latest reply, and I obviously don't have much more, if anything, to state to you on this matter. Also, there is no need to repeatedly link my username; that is perhaps why I wasn't alerted via WP:Echo that you had. It's like a bad case of WP:OVERLINKING, except applied to discussion between editors (if you didn't know about that article guideline before, you do now). And it is not like I am not watching this article/talk page. Flyer22 (talk) 11:10, 22 September 2013 (UTC)

Sorry about (apparently) overlinking your username... some of this linking was there to avoid the awkward "he or she," but now that, at least, is not necessary. I should have just checked your user page, of course... again, sorry.

Let me also assure you that if I really misrepresented your motives or comments, it was done in good faith---what I wrote was my best guess as to where you were coming from. Just as importantly, I do believe you are writing in good faith, too. It's simply that just as you don't understand my logic, I don't understand yours. Perhaps it is indeed best to disengage from this argument for some time... but if, in the future, it occurs to you that there is some different way to get your point across to me, which you haven't tried so far, I hope you will attempt to do so. Reuqr (talk) 15:24, 22 September 2013 (UTC)

I don't think the use of homology in the evolutionary and developmental (or even chromosomal) sense are homonyms; they refer to shared ancestry. On the other hand, after reading this discussion (which I feel is slightly getting out of hand) I am starting to lean towards developmental homology having its own page (if one at all). I guess I'm changing my opinion if that's alright.

First, I definitely wouldn't want to merge homologous chromosomes with this page. We call copies of a chromosome homologous, but we don't refer to the genes on each homologous chromosome as being homologous: they're simply the same gene (think about recombination).

Second, It is certainly easy to craft a definition that neatly fits both the evolutionary and developmental definitions (I'll leave the debate over whether such a definition is POV to others), but really the two fields don't overlap that much. It should also be pointed out that "developmental homology" can also (and most likely does) refer to similarities in the embryonic development between different organisms i.e. among mammals.

In my opinion, as a biologist, "developmental" homology shouldn't have it's own page: it should be described in the context of sexual differentiation. I believe it would fit rather nicely there, and add quite a bit to that article. Dopeytaylor (talk) 19:03, 4 October 2013 (UTC)

Hello again, Dopeytaylor. In what way do you feel that this discussion is slightly getting out of hand? And you would want to remove any mention/detail of the sexual differentiation aspect of homology from this article? If so, I cannot agree with that. Various articles that link here are referring to the sexual differentiation aspect of homology; readers should not be pointed to the Sexual differentiation article instead of an article about homology in those cases, especially when the words homology, homologue or homologous are being used. Flyer22 (talk) 19:22, 4 October 2013 (UTC)

I think the problem is that "Homology" in a biological context, gets applied to anything that shares an origin in spite of subsequent differences. That could be homologous chromosomes, the homology between a bat's wing and a human arm, or the homology between reproductive structures between the sexes. However, the terms appears to be used differently at the cell-level and below (homologous chromosomes, homologous sequences), compared to at the organ/organism level (sexually/evolutionarily homologous structures).

IMHO, if we're going to split the page, it should be between "levels" - genetic stuff in one, organ/organismal in the other - since the organismal-level homologies are all unified by a developmental basis (across varying degrees of time and relatedness), while I'm not aware of such a unifying principle of molecular-level uses of the term (though this appears to be more your area than mine, Dope). As it stands, the two don't really "mesh" well in a single page. HCA (talk) 19:35, 4 October 2013 (UTC)

HCA, I have to disagree with the distinction you are making. The term is not used differently at the cell-level and below, in fact, historically, sequence homology shares more with anatomical homology (as described in this article). Haemoglobin genes in bats and humans are homologous because they are derived from the same ancestor gene in exactly the same way a bat's wing and a human's arm are derived from the same ancestral structure; which I might add arise in the form they do because of the genes that code for them! In this context we're talking about patters of relatedness that can stretch across millions of years. Homologous sequences can be found in Yeast and Human, who shared a common ancestor a very very long time ago. These are both evolutionary concepts. The only difference between the anatomical and sequence frameworks is that it is much more difficult to talk about paralogous structures in the same way we talk about paralogous genes.

Developmental homology shares less with the evolutionary definition (both anatomical and sequence) because it is not necessarily concerned with the relationship of sequences or physical traits across different organisms (or within organisms in the case of within-species paralogs) and a long period of time, but differences in the way sexes develop. Developmental homology has very little to do with evolution, although evolution can probably explain a lot about it. Dopeytaylor (talk) 07:23, 8 October 2013 (UTC)

To some extent, it's just in how you split it, and the emphasis on mechanism vs history (though the two are, of course, interrelated).

By "developmental homology" are you referring to only to homologies within a species (between sexes of vertebrates or castes of social insects), or also to the developmental homologies that underlie anatomical homology? Because really, they're two sides of the same coin - changes in morphology due to modifications of the same fundamental developmental program. As you correctly note, sequence homologies go back way further, since species with totally different developmental programs (or lack of them at all, in unicellular species) still all use DNA, while species with totally different developmental processes (plants vs humans) logically cannot have developmental homologies.

IMHO, this suggests that both mechanism *and* history are important in understanding different types of homology (and why they differ), suggesting in turn that it may be better to keep the page unified and collaborate on a better lede and introduction. HCA (talk) 23:57, 8 October 2013 (UTC)

HCA, in it's present form in the article "developmental homology" is defined in the context of "homology between genders and forms" and "sexual differentiation." If you look into the literature "developmental homology" refers to, as a rough example, how you can start with a blastocyst that is identical for humans and mice (as one example), and end up with something different (or similar) later on ( in order to place these definitions in a broader context see these references here, here, here, here and here). The definition you find in this article is narrow, and arguably, fits more specifically into the context of sexual differentiation solely.

With regards to what kind of ontology we'd like to enforce on homology we can surely split the concept into three, potentially hierarchical, domains; sequence -> developmental -> anatomical. DNA contains genes (with homology relationships), which when expressed (or not expressed) give rise to developmental pathways (with homology relationships) that result in anatomical traits (with homology relationships). Of course we should keep in mind, while this is a convenient conceptual construct, there will be exceptions i.e. pathways can control the expression of genes etc.

So, while I am alright with keeping "developmental homology" in this article, I suppose the section needs to be written with a broader, historically aware (I'll admit I'm still sifting through the literature on the subject) definition. I would not argue that sexual differentiation should be kept out all together, but it should not play a central role. Dopeytaylor (talk) 15:28, 9 October 2013 (UTC)

I obviously wouldn't argue that the sexual differentiation aspect should not play a central role, but it already doesn't play a central role. There is mention of it in the lead and one very small section about it lower in the article, a section that, as you seem to agree, needs expansion. Flyer22 (talk) 09:37, 10 October 2013 (UTC)

I'll chip in my two cents precisely because I am not a biologist. I know from wikipedifying about my own areas of specialization (math, comp. sci., ...) that we need to remind ourselves that Wikipedia is not intended as a graduate-level text, let alone a collection of research monographs. My point is that, although we certainly wish an article on a technical topic to be accurate and aligned with the most recent science, we also wish it to be aimed adequately at a broad audience of nonspecialists. And it is from that perspective that I cast my vote in favor of splitting the article. I see that the two senses are closely related—dare I say homologous?—but their meaning and usage are sufficiently distinct as to cause some confusion for the nonexperts.—PaulTanenbaum (talk) 18:51, 22 January 2014 (UTC)

I am chipping in my two cents too. I am female too, and am familiar with my own anatomy. I am familiar with male anatomy based on close inspection. I just read this, Quora on scrotum to labia majora homology. It linked to this article, which made me raise an eyebrow. Then I read this thread. I think the article should be split. The two concepts are indeed linguistically homologous, but not biologically homologous. as PaulTanenbaum said. Wikipedia addresses that with disambiguation pages. This needs to be addressed as such. I concur with Paul.--FeralOink (talk) 19:44, 22 May 2014 (UTC)

Tables

some of these tables seem unnecessary; specifically the one on plants and in the sexual-differentation section. Unless they are improved I believe the should be removed.Dopeytaylor (talk) 20:20, 16 September 2013 (UTC)

The tables seem to be there to provide examples. I feel that examples are important/helpful in this case, but they can be presented in prose...without being placed in tables. And not all of the examples are needed, of course. Flyer22 (talk) 02:04, 18 September 2013 (UTC)

Different development pathways underlying homologous structures

In his 1971 work "Homology: An Unsolved Problem", evolutionary embyrologist Gavin de Beers stated that:

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It is now clear that the pride with which it was assumed that the inheritance of homologous structures from a common ancestor explained homology was misplaced, for such inheritance cannot be ascribed to identity of genes. The attempt to find 'homologous' genes, except in closely related species, has been given up as hopeless.

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Based on my own experience, for awhile I just assumed homologous structures developed from the same genetic development pathways because I never saw anything to the contrary mentioned in any discussion on homology. I think this distinction should be clarified in the article. 70.16.210.145 (talk) 01:12, 5 March 2014 (UTC)

Assessment comment

The comment(s) below were originally left at Talk:Homology (biology)/Comments, and are posted here for posterity. Following several discussions in past years, these subpages are now deprecated. The comments may be irrelevant or outdated; if so, please feel free to remove this section.

Rated "top" as highschool/SAT biology content; important concept in biology/evolution. - tameeria 04:55, 9 March 2007 (UTC)

Last edited at 04:55, 9 March 2007 (UTC). Substituted at 18:12, 29 April 2016 (UTC)