Talk:Model organism

Uncategorized early comments

I think it might be useful to restructure the list of model organisms into two redundant lists--one grouped by classification (bacteria, plant, animal, etc.), as it is now, and the other grouped by the field which makes use of it (genetics, cell biology, neurobiology, developmental biology, agriculture, etc.) IlliniWikipedian 17:42, 18 June 2006 (UTC)

History of the term?

When did the term "model organism" come about in literature? Does anyone have a timeline of usage and increasing usage? --Cyberman (talk) 01:14, 5 November 2009 (UTC)

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I was looking for "zebrafish", and was a little bit confused by "zebra danio". According to my experience and a quick search of the literature, "zebrafish" and "Danio rerio" are by far the most common words used by scientists to discuss the creature that this page refers to as "zebra danio" and "Brachydanio rerio".

Interestingly, it seems that researchers either use "zebrafish" AND "Danio rerio" or they use "zebra danio" AND "Brachydanio rerio". A BIOSIS search for "zebrafish" turned up 4427 articles, while a search for "zebra danio" turned up only 34 articles.

-adam

Hm. If you have better refs and think it is wrong then by all means change it. Fish names are hard to pin down and seem to change with each passing generation of researchers. Common names are a mess too. --mav

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I don't agree with the opening sentence. Researchers do consider potential economic benefits when choosing their model systems. This is necessary because funding agencies often take this into consideration and the researcher does need to get grants. I propose that the defining characteristic of a model organism is that it is studied as an example of a larger set of organisms. Economic benefit is one of many considerations that a researcher takes into account when choosing an organism. AdamRetchless 01:24, 17 Mar 2004 (UTC)

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One thing that we need to express is that there are many model organisms, and that different ones are used in different fields and differnt time periods. Listing every model organism ever used would not be worthwhile, so we need to prioritize. One obvious means of prioritizing would be to list the most common model organisms. However, I think that will tend to bias the list towards molecular biology (as the list currently is). Perhaps we could list organisms by field (Microbiology, Development, Neuroscience, Ecology, Genetics) AdamRetchless 01:24, 17 Mar 2004 (UTC)

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I think the goldfish may be a common model organism but I am not sure.--βjweþþ (talk) 19:07, 20 January 2006 (UTC)

I disagree with the part where humans are listed under model organisms!

embryology

would sympathtic editors consider a positive vote here? [1]Slrubenstein | Talk 15:34, 23 August 2006 (UTC)

Merge Proposal

• Support Addhoc 12:43, 11 November 2006 (UTC)
• Against. A model organism is a well-known, widely used organism in research, like the worm, the fly, the zebrafish and so on. An animal model, on the other hand, is a condition studied in an animal, for example MPTP-induced parkinsonism, metrazol-induced epilepsy, and many others. Dr Zak 19:11, 15 November 2006 (UTC)
• Against - (per Dr. Zak and Ragesoss). I like Dr Zak's distinction! I also see a fair amount of interchangeable usage between each term (Animal Model and Model Organism). (Of course, this doesn't mean the world is using the terms properly or consistently.) For instance, this link [2] appears to use the term Animal Model the way WP's Model Organism is currently written. Also, Google quickly tells us that Animal Model is the name of a specific USDA procedure ... something I don't see mentioned on WP's Animal Model article. (Please see [3] --Keesiewonder 03:06, 29 November 2006 (UTC) (Moved vote from moderately against to against. Keesiewonder 14:22, 3 December 2006 (UTC))
• Against; Dr. Zak puts it well. But animal model should be coordinated more closely with this article, and should note the partial overlap between the two concepts.--ragesoss 21:05, 2 December 2006 (UTC)
• Against. Yes, Dr. Zak does put it well. However, I believe that there is a difference as Model organism has a more biological side to it, whereas Animal model focuses more on the psychological and sociological side.--reverandspaniel 12:52, 5 January 2007 (GMT)
• Against as per above, not to mention that the material on animal models would be drowned out by all the non-animal model organisms. Bendž|Ť 10:10, 19 July 2007 (UTC)
• Against for reasons stated above. I think we can safely remove the merger proposal. —Preceding unsigned comment added by Chodges (talk • contribs) 18:46, 18 August 2007 (UTC)

Citation needed?

"This strategy is made possible by the common descent of all living organisms, and the conservation of metabolic and developmental pathways and genetic material over the course of evolution." (Opening paragraph)

Does this really need a citaion? —Preceding unsigned comment added by 129.67.82.145 (talk) 09:18, 19 July 2007

• I don't think it needs a citation, as it is in the lead section, isn't even slightly controversial, and can be understood by going to the linked pages. I'm removing the fact tag now. If anyone really wants a citation, please explain what you'd want the citation to say. I can see using sources for the fact of common descent, the similarity of metabolism, the conservation of developmental pathways, and the conservation of the genetic code throughout evolution, but that would be FOUR inline citations for one sentence in a lead section, and I simply can't see that doing any readers any good Enuja 02:57, 17 August 2007 (UTC)

As far as I'm concerned it's uncontroversial, but that's far from the case in some parts of the world. I'm not reinstating the tag, but if somebody requests a citation, it should be given. As with many "obvious" statements, surely there's a review article or book that could be refered to instead of four separate citations. Bendž|Ť 10:16, 19 August 2007 (UTC)

Well, I spent a few hours looking for review articles, and I found only technical ones about HOW useful models are, not general ones that give the very basic justification for the generalizability of biological research. So I went to the library and got Michael Allen Fox's book The Case for Animal Experimention: An Evolutionary and Ethical Perspective, skimmed it last night, and used it as a reference today. I'm not convinced that it's the best reference, as the relevant information is mostly on a few pages in Ch 2 but is honestly spread throughout the book, and most of the book is not relevant to this statement. If anyone can find a better reference, by all means substitute it, but this statement simply can't sit around with a fact tag on it. When people who know nothing about the subject see a fact tag, they think that the fact is in dispute, and this fact is simply so basic that it's really hard to find a concise reference for it. Enuja 19:41, 20 August 2007 (UTC)

Virus as organism?

I'm about to amend the reference to one of the model viruses as an organism. Strictly speaking viruses aren't organisms. If fact, a virus particle can't really be described as 'living'. i.e. it has no independent life. However, as a shorthand I do see the value in referring to an organism for simplicity - its just that inaccuracy in terminology bugs me! —The preceding unsigned comment was added by 82.211.95.178 (talk) 15:09, August 21, 2007 (UTC)

What alternative terminology do you suggest? I know evolutionary biologists who work on viruses, and think of their model systems as organisms. Honestly, most biologists don't worry about what is defined as an "organism" or not; we just study them. I recently came across a philosophy of biology paper that claimed to defend why biologists aren't worried that we really don't have a good definition of organism, but I didn't read the paper. Enuja 17:26, 21 August 2007 (UTC)

I totally disagree, Enuja. Just about all of the bioligists I know would be embarrassed to refer to a list of "organisms" and find a virus on it. I don't really have a solution, perhaps "model systems" instead of "model organisms", but that sacrifices clarity. To me, it sticks out like Ella Fitzgerald in the Vienna Boys Choir.173.8.220.209 (talk) 16:31, 2 March 2009 (UTC)

cleanup?

I cant see reason for the tag clenup from November. Could'nt anyone provide some objections, regarding the style of the article, which could be followed to reach desired standard? If not I will remove the tag after several days, I do not realize any violation of manual of style here.

In fact I thought that this tag is given usually to the articles, which are messed up in style more seriously and do not reach any grade in the quality assessment. This one was evaluated as B class. So it does not fit to me together. Reo ^ON | +++ 18:19, 8 March 2008 (UTC)

Removed Reo ^ON | +++ 20:21, 30 March 2008 (UTC)

Coleochaete

This genus of algae is used as a model organism - see the article. Should it be included here too? Smartse (talk) 17:46, 16 April 2009 (UTC)

I myself am seeing Coleochaete as potentially great model organism in plant developmental biology, - nowadays promoted by the group of Hasseloff (I see all the arguments as valid and I could provide some additional..). But otherways it is still not probably widely accepted by wider comunity of plant biologists. For what I know about this model, I think it is just question of time and it will become serious one. But as it is for the moment, ... I think it still is not such model organism to be relevant in encyclopedia. I am little hesitating here. To put it in other words, if we will wait, we will spoil nothing, the time can help here to judge its relevance. Reo ^ON | +++ 20:06, 23 September 2009 (UTC)

I should rather say that the plant biologists are simply not aware of the model potential, then say that they do not accept it. Please lets take it as my correction. Most plant biologist as it is now do not recognise either any organisms before the bryophytes or they are aware just of existence of Chlamydomonas, because it had been sequenced. But only tiny number of them has any awareness of phylogenetic relationships in between algae and potential importance in the comparative works. But this seemingly begins to change. There are some stirs in plant biology and the awareness seems to slowly come to existence. In just 2 last years I saw several independent articles on differnt topics first time implement this strategy. So we will see in the future, whether the comunity will for this aim adapt coleochaete as an model. Reo ^ON | +++ 20:14, 23 September 2009 (UTC)

Xenopus sequence

In the table comparing model organisms, Xenopus is listed as having been sequenced. However, as the linked ref states, only X. tropicalis has been determined - not X. laevis. I imagine we'll know laevis' genome soon enough, but at the moment the table isn't correct. Perhaps it should say "in progress" or words to that effect? Shawthorn (talk) 09:22, 26 June 2010 (UTC)

Table of model genetic organisms - biochemistry

I had put tags {{fact}}{{dubious}} to the Arabidopsis biochemistry field in the Table of model genetic organisms. I dispute the statement.

The table is excelent idea and overview of basic - important properties of model organisms (I mean well chosen), but what are the sources for the claims? Especially for the rather subjective part of the state of knowledge of the organism's biochemical pathways?

What "makes" Arabidopsis's biochemsitry poorly understood and Physcomitrella's excellent in comparison? Not just in comparison to the moss model Physcomitrella,- but in comparison to any other model in the table? I work in plant physiology research, so the contrasting assesment for the two plant models is most striking for me, i can not easily compare the depth of knowledge of biochemistry between Arabidopsis and Xenopus, for example (But who can actually?), but the "poor" assesment of Arabidopsis biochemistry pathways looked a bit strange to me all the time.

In plant biology research there is no model so much studied as Arabidopsis. We cannot say its pathways are perfectly understood just because it is hardly possible to claim it about any other higher organisms (or we can?). There is never ending ambundance of possible biochemical reactions in living organism that it looks not very well if we would claim, the excellent knowledge about any of them. That might probably just in comparison to other studied model organisms.

What do You think about this assesment scale and, what should we do to ensure valid informations in the table? Requirements? Reo ⁺ 20:19, 2 March 2011 (UTC)

The column should be deleted. It’s completely subjective and uncited. Even if it was cited to a review or textbook that compared model organisms, I’d question it’s value, it means nothing to say that the knowledge of the biochemistry of an organism is ‘excellent’. Particularly odd is the ‘not so good’ for C. elegans.Franmars (talk) 16:27, 24 March 2011 (UTC)

Thanks for your reply and position. I completely understand (and agree) why to weed it out, but I am undecided right now, whether to delete it completely or replace it by somehow better formulated alternative. Now, now I have found quite a new and very good article exactly to the topic - 2010 Müller and Grossniklaus - Model organisms — A historical perspective, interestingly there is also list of model organisms with percentually quantified proteome coverage. Arabidopsis thaliana got 50 %, Mus musculus have 34% and C. elegans got 68%. Interesting. It can be helpfull to this article on many fronts. (I would have to read it anyway, I hope I will have time to incorporate something here) Reo ⁺ 04:06, 6 April 2011 (UTC)

There probably would be some columns worth adding to the table, for the time being I’m going to delete the column as it really is pretty useless. Proteome coverage could be worthwhile. There could probably be some more coverage about the genomes, maybe genome size and predicted numbers of genes? Franmars (talk) 13:58, 13 April 2011 (UTC)

SEPARATE SUGGESTION: In the Table of model genetic organisms, it's be helpful to see another column with common names of the organisms. — Preceding unsigned comment added by MBVECO (talk • contribs) 20:37, 9 December 2015 (UTC)

Text removed for now

A recent edit added the following to the See also section, which I have removed for now.

• dcGO (dcGO), a database of protein domain-centric ontologies including the PSnet utility for cross-linking several phenotypes in major model organisms.Fang, H.; Gough, J. (2012). "DcGO: Database of domain-centric ontologies on functions, phenotypes, diseases and more". Nucleic Acids Research. 41 (Database issue): D536–D544. doi:10.1093/nar/gks1080. PMC 3531119. PMID 23161684.

The problems as I see them are (1) dcGO is not yet a page that can be linked to, so doesn't belong on the See also section, (2) the concept of protein domain-centric ontologies is not covered in wikipedia, which currently deals with the philosophical and computational concepts of ontologies. This therefore, is not readable material suitable for the encyclopedia. Sminthopsis84 (talk) 16:38, 5 December 2012 (UTC)

Good there. You are right.

Most importantly, you are completelly right regarding 1)

Regarding 2) ... Gene Ontology we do have, and it is not such weird and exotic concept. It is quite enough connected to the function of model organisms also, because only through correct choice of models the ontology can be reconstructed. --Reo ⁺ 21:14, 6 December 2012 (UTC)

Okay, some explanation would still be needed to bridge the gap between gene and protein domain, since some readers might come to this page with zero knowledge of genetics. Sminthopsis84 (talk) 21:38, 6 December 2012 (UTC)

Homologous recombination

I've boldly removed the column of a table that listed without adequate explanation a yes/no presence of homologous recombination. It was full of errors, e.g., that E. coli supposedly has the mechanism, and for various other organisms there had clearly been confusion between whether the mechanism is present and whether it can readily be used for targeted gene insertion (e.g., Chlamydomonas). Such a table column might make sense to a few people working on a variety of model organisms, but error-prone as it was, I think wikipedia is better without it. Sminthopsis84 (talk) 18:43, 13 March 2013 (UTC)

Model organisms used for specific objectives

This section of the article seems abrupt, like 3 random areas of study were selected. Maybe make the categories broader, like "sexual", "ecological", "developmental" etc. so it covers more of the diversity of fields of study that use model organisms. Jtrivedi92 (talk) 00:38, 4 February 2014 (UTC)

Locust?

Perhaps the locust should be listed? It seems to have been widely used; perhaps less so now outside schools? "The relative size and robustness of the locust make it simple to handle and ideal for such [educational] investigations." I note that a recent paper described its use as "novel", so perhaps memories in these days of micro-everything are short. Chiswick Chap (talk) 06:06, 2 April 2015 (UTC)

References

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