Talk:Homology (biology)

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

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[edit] 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)

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

[edit] 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)

[edit] 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)

[edit] 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)

[edit] 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)

[edit] 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)

[edit] 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.'

[edit] Xenolog

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

i've found a definition: Xenolog: Homolog acquired by lateral gene transfer. from [2] -Sucrine ( ><> talk) 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)

[edit] 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."

[edit] 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)

[edit] 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!

[edit] 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)


[edit] Headline text

SOME DESCRIPTIONS ARE RELATED BY (# CRONOLOGIST 1.PE Sheafield 26/27 2.GUESS 3.PE sime UEP HQ 3.I-POlp.HEL.0 4.USJ 10 Padat No.1 5.3*240mm —Preceding unsigned comment added by 124.82.184.225 (talk) 12:02, 13 May 2008 (UTC)