Talk:Phenome/Redirecting page to Phenotype

Redirecting page to Phenotype

This page should be redirected to phenotype. "Phenome" is just a new word (and quite correctly has been transwikified to Wiktionary, see above) without any real meaning. The definition given in the stub is rather meaningless: "A phenome includes phenotypic traits due to either genetic or environmental influences". Really???? This implies that a "phenome" does not include phenotypic traits that are NOT due to either genetic or environmental influences. Ever heard of anything like that?? "Phenome" has been used in some scientific articles, and is being used by people that either don't know what they are talking about or just want to sound interesting. The word has not any meaning that is different from "phenotype". Note that "phenotype" can be understood as encompassing all traits that can be measured on an organism. In that sense, "phenome" is just a synonym for "phenotype". --Crusio (talk) 11:16, 22 November 2009 (UTC)

The Phenome is to Phenotype as Genome is to Genotype. I am mystified why you think it is the same as Phenotype. Why not redirect Genome to Genotype? It also seems quite insulting to say that the many scientists who have used the term "don't know what they are talking about"? Please try a search on the term "phenome" at Pubmed http://www.ncbi.nlm.nih.gov/sites/entrez and you will see what I mean.--Pfjoseph (talk) 02:59, 17 January 2010 (UTC)

• "They don't know what they're talking about": your words, not mine. I just went through PubMed and read all abstracts using the word "phenome" in 2009. It is quite evident that each and every one uses "phenome" in the sense of "phenotypes". That is quite different for "genome", where people study, for example, interacting gene networks, something very different than just a bunch of studies on each individual gene separately. In "phenomics", people just study more-than-one phenotype, but the level of analysis stays at the level of the individual phenotype. That is why there is, at this point, not a "phenome" and not a science of "phenomics". --Crusio (talk) 04:37, 17 January 2010 (UTC)

Dear Crusio: the phrase "don't know what they're talking about" is taken directly from your first message, and it sounds just as insulting as when I first read it. In "phenomics", people DO NOT just study one phenotype, and the level of analysis DOES NOT stay at the level of the individual phenotype. There are now several pheonome databases that are "analyzing interacting phenotype networks, something very different than just a bunch of studies on each individual phenotype separately" (paraphrasing your own words above, about genome and genotype)

As defined in the original entry a phenome is the set of ALL phenotypes expressed by a cell, tissue, organ, organism, or species. A phenome includes phenotypic traits due to either genetic or environmental influences. Again the "Phenome" is not a Phenotype, it is the sum total of all phenotypes of a given organism, under all conditions. Please note that by doing your redirect, you also abolished all of the useful information on Phenome entered by others. I might have felt different if you transferred the original Phenome information from that unit into the Phenotype Unit. In fact, if you try to do that you will immediately see why the two things are NOT the same.

It is true that the word is stil being used in more than one way, but that is typical of new fields as they evolve. All the more reason to allow those who are involved to use Wikipedia as a forum to consolidate the knowledge!

To avoid getting into a fight over this, I am not reverting your original redirect again at this time. But unless you are a widely published world authority on this subject, I am not sure what gives you the right to be the final arbitrator on this subject, in Wikipedia?--Pfjoseph (talk) 15:46, 23 January 2010 (UTC)

P.S. I suggest a compromise. Restore the original Phenome page and then add in your opinions about why you think, at this point, there is not yet a "phenome" and not a science of "phenomics". --98.155.82.132 (talk) 16:06, 23 January 2010 (UTC)

• Unfortunately, I don't think that compromise is feasible, as it would constitute original research. You're right about the "they don't know" comment, but I didn't say none of the people using the word don't know what they talk about: this goes for some, others just want to sound interesting... I have not seen any article using the words "phenome" or "phenomics" that is really new. Over 20 years ago I published a multi-variate analysis of genetic correlations between mouse behavioral phenotypes measured in an open field. I guess I should have called that "phenomics" as I was "analyzing interacting phenotype networks"... In fact, "interacting phenotype networks" are a phenotype themselves. In psychiatric genetics, for example, syndromes like schizophrenia are used as a phenotype. Norman Henderson in his insightful 1979 chapter in the book by Royce and Mos (and Fuller's chapter, too) treat "phenotype" as "the set of observable characteristics" of an organism. Seen that way, "phenome" is indeed just a synonym of "phenotype". Henderson (and Fuller) presented a hierarchy of phenotypes, starting with the DNA sequence at the lowest level and ending with "fitness" at the top level. As for me being the final arbitrator, of course I don't claim to be that, but I have over 30 years of experience in this field and this is my considered, professional opinion. If you still disagree, you could start an RfC ("request for comment") here and see whether enough editors agree with you to overturn my redirect. --Crusio (talk) 11:49, 24 January 2010 (UTC)

Dear Crusio: I am sorry that i have been too busy to followup until now. I have looked over the history of this discussion and I simply don't understand why my compromise is not feasible, as I dont see how it would constitutes "original research". Also I do not think your field studies in mice give you the authority to decide that a term used by many investigators for >10 years can just be arbitrarily disallowed in Wikipedia, abolishing all of the useful information on Phenome entered by several others. Indeed since the last time I wrote the term has been used in the titles of many papers from many investigators (see examples below)

The biological coherence of human phenome databases.Oti M, Huynen MA, Brunner HG.Am J Hum Genet. 2009 Dec;85(6):801-8.PMID: 20004759

Entity/quality-based logical definitions for the human skeletal phenome using PATO.Gkoutos GV, Mungall C, Dolken S, Ashburner M, Lewis S, Hancock J, Schofield P, Kohler S, Robinson PN.Conf Proc IEEE Eng Med Biol Soc. 2009;2009:7069-72.PMID: 19964203

Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism.Nakahigashi K, Toya Y, Ishii N, Soga T, Hasegawa M, Watanabe H, Takai Y, Honma M, Mori H, Tomita M.Mol Syst Biol. 2009;5:306. PMID: 19756045

From the genome to the phenome and back: linking genes with human brain function and structure using genetically informed neuroimaging.Siebner HR, Callicott JH, Sommer T, Mattay VS.Neuroscience. 2009 Nov 24;164(1):1-6.PMID: 19751805

An integrative network approach to map the transcriptome to the phenome. Mehan MR, Nunez-Iglesias J, Kalakrishnan M, Waterman MS, Zhou XJ. J Comput Biol. 2009 Aug;16(8):1023-34.PMID: 19630539

Phenome analysis in plant species using loss-of-function and gain-of-function mutants.Kuromori T, Takahashi S, Kondou Y, Shinozaki K, Matsui M.Plant Cell Physiol. 2009 Jul;50(7):1215-31. Epub 2009 Jun 5. Review.PMID: 19502383

What new cell biology findings could bring to therapeutics: is it time for a phenome-project in Toxoplasma gondii?Meissner M, Klaus K.Mem Inst Oswaldo Cruz. 2009 Mar;104(2):185-9. Review.PMID: 19430642

I also note that the word "Phenome" in Wiktionary is defined as "The whole set of phenotypic entities in a cell, tissue, organ, organisms, and species. This includes phenotypic traits with genotypic origins". Just how is that definition the same as a phenotype?? And if it is a synonym, why does the word Phenome not even appear in the Wikipedia entry on Phenotype? Also, others have no started using the derived term phenomics, in analogy to genomics (see a few examples below). Should phenomics then also be an extended synonym of phenotype?? Should we make a word called "Phenotypics"??

Phenomics of cardiac chloride channels: the systematic study of chloride channel function in the heart.Duan D.J Physiol. 2009 May 15;587(Pt 10):2163-77. Epub 2009 Jan 26. Review.PMID: 19171656

Entity/quality-based logical definitions for the human skeletal phenome using PATO.Gkoutos GV, Mungall C, Dolken S, Ashburner M, Lewis S, Hancock J, Schofield P, Kohler S, Robinson PN.Conf Proc IEEE Eng Med Biol Soc. 2009;2009:7069-72.PMID: 19964203

Genetics and Phenomics of Pendred Syndrome.Bizhanova A, Kopp P.Mol Cell Endocrinol. 2010 Mar 15. [Epub ahead of print]PMID: 20298745

Genetics and phenomics of hypothyroidism due to TSH resistance.Persani L, Calebiro D, Cordella D, Weber G, Gelmini G, Libri D, de Filippis T, Bonomi M.Mol Cell Endocrinol. 2010 Jan 18. [Epub ahead of print]PMID: 20083154

Colloquium papers: Numbering the hairs on our heads: the shared challenge and promise of phenomics.Houle D.Proc Natl Acad Sci U S A. 2010 Jan 26;107 Suppl 1:1793-9. Epub 2009 Oct 26. Review.PMID: 19858477

I dont see why I should be the one to start an RfC to see whether enough editors agree with you to overturn my redirect. This would be taking up a lot of time of a lot of people. I suggest that you should reconsider your position on this issue.

Thank you for your consideration of the points I have raised

--Pfjoseph (talk) 00:51, 21 March 2010 (UTC)

• The classical definition of "phenotype" is something like "all measurable traits of an organism". If you can show me how this differs from "phenomics", you can revert the redirect. The parallel with gene <=> genome is not correct. A gene is (at least up to a certain point) a discrete entity and a genome is the totality of these different entities. However, there is no such thing for "phenotype". A DNA sequence can be regarded as a pheontype. So can body weight, but its constituents (bone density, fat content, etc) are all phenotypes too. In a sense if you want to use the gene <=> genome analogy, then phenotype is more like genome than gene. Science, like all human endeavors, is subject to fashion. At some point "genomics" became fashionable and many articles studying more than 1 gene started using the word genomics, even though what they were describing was nothing of the kind. However, many other articles really did something new than can justifiably be called genomics. Nothing of the sort is happening for "phenomics". "Phenomics databases" are just a collection of phenotypical measures, much like OMIM is a collection of genes. "Phenomics" is and remains just a buzzword and at most this could be mentioned in the article on "phenotype". --Crusio (talk) 09:14, 21 March 2010 (UTC)

Dear Crusio: You did not respond to my comment that the word "Phenome" in Wiktionary is defined as "The whole set of phenotypic entities in a cell, tissue, organ, organisms, and species. This includes phenotypic traits with genotypic origins". How is that definition the same as a phenotype?? And if they are just synonyms, why do the words Phenome and Phenomics not even appear in the Wikipedia entry on Phenotype?

Fashion, buzzword or not, the reality is that numerous scientists are using the words Phenome and Phenomics in the titles and abstracts of numerous papers in many reputable journals - and they all mean something quite different from just an isolated phenotype. Just try replacing these words with "Phenotype" in every title and abstract and it will be obvious what the problem is. Do you want to replace the term Phenomics with "Phenotypics" or the entire phrase "Collecting all the Phenotypes"? OR the term Phenome with "total phenotypes under all conditions". How would this advance thinking in science, as opposed to holding it back?

At this point, the thing speaks for itself, and I am mystified by your resistance. it appears that you just simply dislike the words, for some non-scientific personal reasons. Wikipedia is meant to the inclusive of verifiable knowledge. Why try to block out an entire line of modern thought? I suggest that you do the revert and then let the many other users of Wikipedia chime in with their views. That would be in the spirit of Wikipedia.--98.155.82.132 (talk) 13:40, 24 March 2010 (UTC)

• "The many other users of Wikipedia" that ache to learn about the phenome seem to be limited to yourself... And replace "phenome" with "phenotypes" (plural) in the titles and phrases you mentioned and that will work quite well. --Crusio (talk) 14:15, 24 March 2010 (UTC)

• There is absolutely no cause to be patronizing and insulting. This can happen when a recipient becomes uncomfortable holding his/her position but does not want to admit it. How do you know that other users of Wikipedia would not be interested? By deleting the section from Wikipedia without even mentioning it in the location of the redirect you have effectively eliminated any possibility of finding out? Are you also going to fix the "error" in Wiktionary, to make sure that this "error" is not propogated?

I tried your suggested exercise replacing "phenome" or "phenomics" with "phenotypes" and got the following non-sequiturs:

The biological coherence of human phenotypes databases

Entity/quality-based logical definitions for the human skeletal phenotypes using PATO

Systematic phenotypes analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism

From the genome to the phenotypes and back

An integrative network approach to map the transcriptome to the phenotypes

Phenotypes analysis in plant species using loss-of-function and gain-of-function mutants

What new cell biology findings could bring to therapeutics: is it time for a phenotypes-project in Toxoplasma gondii

Colloquium papers: Numbering the hairs on our heads: the shared challenge and promise of phenotypes

While a few of them might be manipulated further to work, they all take away from the actual meaning that the author intended.

I see that phenomics is also now redirected to phenotype. This is an even bigger stretch, I think. According to Wikipedia, "Synonyms are different words with identical or very similar meanings". The meanings intended by authors who use the terms "phenome" or "phenomics" are most often not the same as phenotype or phenotypes.

I am at a complete loss to understand the logic of your position on this matter. --98.155.82.132 (talk) 02:22, 27 March 2010 (UTC)

• P.S. I looked back on the history of this Wikipedia entry and before I got involved in 2008, there were numerous contributors to the entry, going back to 2004. So your remark that "The many other users of Wikipedia" that ache to learn about the phenome seem to be limited to yourself..." is clearly incorrect. I also notice from your own page that you are involved in several "revert wars". I dont want to start one myself, and I do wish that you would see reason --Pfjoseph (talk) 02:34, 29 March 2010 (UTC)
  • What I meant is since the article was redirected to phenotype, only you seem to object, not anybody else. As for those "revert war" tags on my userpage, they were placed by an irate editor who was objecting to the fact that I reverted his edits, because he was removing among others speedy deletion tags from articles that he created, uploading non-free use images without copyright info, and creating more havoc. An ANI Thread was even opened about this. Things have quieted down there and the tags have been archived. I almost never edit posts from others to my talk page, even if they are unjustified. As for your previous comment about me being condescending and insulting, I don't see anuthing like that in my March 24 comment. Regarding the "phenotypes" will serve well for "phenome" comment, I obviously was not referring to this in a grammatical sense as that obviously won't work (phenotypes being plural and phenome being singular). But: "The biological coherence of human phenotype databases" works pretty well, for example. --Crusio (talk) 08:48, 29 March 2010 (UTC)

• If you cannot recognize that you were being condescending and insulting, that speaks for itself. Diverting the conversation into the fine semantics of prior messages does not change the fact that your position remains intellectually untenable, and that you are simply unwilling to admit it. I remain at a complete loss to understand the logic of your position on this matter, and the only reason I can see why you cling to it is pride. I guess I have no choice but to revert, and hope we do not end up with a revert war.--Pfjoseph (talk) 02:46, 3 April 2010 (UTC)

• Your fine dissection of my motives is most illuminating. --Crusio (talk) 07:45, 3 April 2010 (UTC)

• I will avoid taking any offense at your sarcasm. But I do see that you have directed me to the Wikipedia good faith doctrine. I freely apologize if I have given the impression that I am primarily questioning your motives. Please forgive me. I am primarily questioning the logic of your position on this matter, which seems to ignore what is happening in the real world. A Google scholar search of the term "Phenome" yields 76,500 entries, and a quick check suggests that more than half of them are valid entries, and in most cases, substituting phenotype(s) would not work, or would render the writers meaning much more obscure. The bottom line is that while you seem to dislike the term very much, it is here to stay, and more and more people are using it, to mean something different from phenotype(s). I request that you let me revert, and allow other readers to chime in if they have opinions on the matter. This would be in the best interests of Wikipedia, I think.--Pfjoseph (talk) 00:07, 12 April 2010 (UTC)

• Other people can chime in to this discussion any time they want. Fact is that many people must have searched for the term "phenome" and did not object to being redirected to phenotype. As soon as somebody comes up with a meaning for the word that really means something different than phenotype or phenotypes, I'll drop my resistance to its use. I just spent three days at a meeting on "systems genetics" and the genetic analysis of complex traits and nobody used the word "phenome" or "phenomics" (although they did use the just as ugly neologism "phenotyping"). This in a meeting where people discussed studying hudreds or even thousands of genes and phenotypes simultaneously. --Crusio (talk) 07:27, 12 April 2010 (UTC)

• The way you have done the redirect ensures that no one will know what happened. If I search Phenome in Wikipedia, I just get the Phenotype page. If I then search all the tabs in the Phenotype page there is no mention of the word Phenome! So a new reader has no easy way of finding the original redirect and your explanation and logic behind it. And finding this particular Talk page to add any comment to it is very difficult (I had to bookmark it to find it again). Thus, while you might not have intended to do so, you have squelched any debate on this issue, by making it too difficult to find out what you have done. As for the definition of the term, it is at http://en.wiktionary.org/wiki/phenome. Finally the description of your involvement in "systems genetics" (ugly neologism, in my opinion!) explains a lot. Genetic determinists simply cannot bring themselves to accept the reality that genes are not all powerful. So, Genome, Genomics and Genotyping are all good words, but Phenome, Phenomics and Phenotyping are not? How is that an intellectually justifiable position? If you wish to support your position intellectually in Wikipedia, please make an entry into the Phenotype page listing the words Phenome, Phenomics and Phenotyping, and explaining why you feel that these terms should never be used by anyone ever again, and providing a good rationale for this. --Pfjoseph (talk) 12:15, 16 April 2010 (UTC)

• It's strange how you keep making assumptions about my motives that are all wrong. Have a look at my publication record and you'll see that I may be many things, but not a genetic determinist... (The characters I work with have a heritability of about 50% max, but often much less). As for systems genetics being an ugly neologism, I agree, but I was not the one naming the consortium. The comparison between gene <=> phene does not work. A gene (or at least a DNA sequence) is an unambiguous entity. A phenotype can be any character that a researcher chooses to measure. It can be eye color, or the frequency of the light that an iris reflects, or anything else. Whereas genes are determined (let's not go into subtleties like methylation and such), phenotypes are not. For a given organism, it's genome is bounded because there is a limit to the amount of DNA (and number of possible genotypes) it has. It's "phenome" is not bounded and undefinable, because phenotypes are defined by us, the researchers. Body weight, for example, is a perfectly valid phenotype. But you can dissect it further: amount of adipose tissue, bone density, etc, and each of those characters is again a phenotype in its own right. In any case, this discussion is really growing stale, so unless you come up with new arguments, I don't intend to answer these postings any more. As before, an RfC is still a possibility that you may try. --Crusio (talk) 12:43, 16 April 2010 (UTC)

• As always you completely ignore the main points and suggestions I am making, do not answer any of my direct questions, and return instead to your fixed unyielding view that you are right and that hundreds of other researchers are not. I should have realized that it was hopelesss, once you said that even the word "phenotyping" was not acceptable (almost 5000 entries in Pubmed, >100,000 entries each in Google Scholar!). Are you also going to redirect http://en.wikipedia.org/wiki/Systems_biology ? I fully agree that this is an intellectually stale discussion, but that is because you will not enter into a dialogue with give and take, you just keep restating your fixed position, and ignoring all the valid issues I raise. I will wait a bit to see if you at least follow my request to make an entry into the Phenotype page listing the words Phenome, Phenomics and Phenotyping, and explaining why you feel that these terms should never be used by anyone ever again, and providing a good rationale for this. In my opinion, that would be the intellectually honest thing to do, rather than completely obscuring what you have done.--Pfjoseph (talk) 15:24, 18 April 2010 (UTC)

• P.S. I just noticed that the Phenotype page actually now has External links from others to
• High Throughput Phenotyping Systems
• The Plant Phenomics Platform. Video
• Mouse Phenome Database

To be through, you should also delete all of these.--Pfjoseph (talk) 15:31, 18 April 2010 (UTC)