Talk:Phenome

A request

Just a request, I've stumbled into this area by accident, and I'd like to do what I can to calm things down a bit. Could we not force the redirect for the time being, and have some further discussion? I don't have a sense as to whether the redirect is a good or bad idea, but this is approaching an edit war. Thoughts? --Nuujinn (talk) 19:37, 1 May 2010 (UTC)

• Sounds good to me. --Crusio (talk) 19:58, 1 May 2010 (UTC)

Keep, Redirect, or Convert

First of all, I've archived the prior discussion here, just for housecleaning purposes. There is a lot of good information in there, it's worth reading through.

Second, I'm not an expert in this topic--my prior field of study was philosophy of language and literary criticism, and I work in IT. So I'm very familiar with jargon.

In terms of defining the problem, I believe we have two basically independent issues to consider:

• Is Phenome essentially a synonym of Phenotype?
• Is Phenome in wide enough use to justify an article on it?

I note that User:Colonel Warden has made some edits, and found a reference that dates to 1949, so it is clear that the term has a long history. I also note that User:Crusio has made some compelling arguments in the archive that the term is essentially jargon, and really just a synonym of Phenotype. There's also a third related term, Phenomics, and from what I've read, it seems that there is justification for that article, if only for the reason that there are now centers and groups using that term in their titles.

I also think at this point we have three main options:

• Redirect this page to phenotype
• Maintain this page and improve it
• Change this page to a disambiguation page linking to Phenotype and Phenomics

Given User:Colonel Warden's recent edit, my inclination is to maintain this page and improve it. What does everyone else think? --Nuujinn (talk) 15:33, 2 May 2010 (UTC)

• I am glad to see that several others feel the same way as I do about Crusio's redirect of the Word Phenome to Phenotype. As you can see from the archived discussion here, I spent a long time trying to reason with him on the point, but ran into a brick wall. If you read the discussion, it will be clear why:
• Phenome is NOT just a synonym of Phenotype.
• The use of Phenome is indeed wide enough and different enouch to justify an article

I am glad to see that the page has been restored, but am a bit concerned that some of the original useful information on the page got deleted in the process. Anyway, I have no axe to grind, and hope that the more expert users will help restore more of the original useful information.--Pfjoseph (talk) 14:19, 9 May 2010 (UTC)

Well, I feel strong sympathy to his position as well. In terms of denotation, I think they are synonyms, but I also see that folks are trying to distinguish the two. My impression is that as a term, phenome is at this point just really jargon and not well defined, but will become more entrenched over time, and hopefully a clearer distinction will emerge. Such shifts are not unusual--I see the same issues with Bioinformatics as a term, for example. But in any case, whatever our opinions, it's the sources that count, so anything sourced is welcome. Feel free to bring material here to discuss additions, or be bold and put anything referenced in. --Nuujinn (talk) 14:33, 9 May 2010 (UTC)

• As an example for sources, a search of "Phenome NOT Phenomena" at Pubmed http://www.ncbi.nlm.nih.gov/PubMed gives ~100 relevant citations in respected journals, beginning in 1998, and with many being added in recent times. It may have been "jargon" to begin with, but it is now in common usage, to mean something different from Phenotype. Some of these citation were in the original version, but were removed in the process of redirection and subsequent reversion--Pfjoseph (talk) 12:29, 14 May 2010 (UTC)

I agree it common usage, but I'm not at all sure it's well defined or all that distinct from Phenotype. But ultimately that doesn't matter, feel free to bring in additional sources or restore older ones if you think that will improve the article. --Nuujinn (talk) 15:35, 14 May 2010 (UTC)

Accuracy

• This article is still a mess. there is (not unsurprisingly, I think) no clear definition of phenome. As the set of all characteristics displayed by an organism is its phenotype, there's some overlap here. In addition, a phenotype is an "observable characteristic" and as such it is difficult to speak about the "phenotype" of a species... --Crusio (talk) 14:25, 10 March 2011 (UTC)

The systemic approach

I've seen, in the Talk page, there is a clear explanation of the difference between "phenome" and "phenotype" (by comparison with "genome" and "genotype"). What is missing here (and in the Phenome explanation!) is the underlying systemic approach in phenomics (see http://en.wiki.x.io/wiki/Systems_biology; you'll see there references to "general systems theory"), meaning the view of an organism as a "dynamic system" (dynamic≈changing; sistem ≈a structural integrated "whole") entity which changes, modifies itself under the influence of the exterior factors in the scope of maintaining its internal stability (its "life"). Concerning the internal factors, don't forget a livig entity is, in fact, "a system of systems" where are the decreasing complexity levels:

the medical systems (nervous, locomotor etc.)
the organs (heart, liver, brain etc.)
the organ components (cerebelum, etc)
...
the cell
...
the atoms
... 
The fundamental "bricks" of universe,

and everyone of this sub-systemes, at its own level (biology, chemistry, physics), acts as a dynamic system!. As regards the relation between "phenome" and "phenotype", I think the "phenotype" is the static (at a certain point of time) expression of the "phenome". So, I think the page must be maintained and improved with the systemic approach.Gillcv (talk) 12:32, 3 October 2011 (UTC)

• Phenotype is not necessarily static. There have been genetic analyses of phenotypes like changes during development (weight gain, for example). And, of course, a phenotype is the totality of observable characteristics of an organism. That obviously includes dynamic aspects. --Crusio (talk) 15:15, 3 October 2011 (UTC)
  

• Let me be a little more explicit!

i/ See "The Genotype/Phenotype Distinction" at Stanford Encyclopedia of Philosophy;

It is essential to distinguish the descriptors of the organism, its genotype and phenotype, from the material objects that are being described. The genotype is the descriptor of the genome which is the set of physical DNA molecules inherited from the organism's parents. The phenotype is the descriptor of the phenome, the manifest physical properties of the organism, its physiology, morphology and behavior

So this is a philosophycal (linguistic reflected) distinction between the "object" (phoneme) and its "description" (phenotype).

ii/ As regards the relationship between "structure" and "functionality" of an "object" and the necessity to view this object as a dynamic system let the biologists speak;

a/ Wolkenhauer O (2001) Systems biology: The reincarnation of systems theory applied in biology? Brief Bioinform 2:258–270. [1]

Systems biology is an emerging field of biological research that aims at a system-level understanding of genetic or metabolic pathways by investigating interrelationships (organisation or structure) and interactions (dynamics or behaviour) of genes, proteins and metabolites.

Genomics is the field of biological research taking us from the DNA sequence of a gene to a structure of the product for which it codes (usually a protein) to the activity of that protein and its function within a cell and, ultimately, the organism. Crossing several scale-layers from molecules to organisms, we find that organisms, cells, genes and proteins are defined as complex structures of interdependent and subordinate components whose relationships and properties are largely determined by their function in the whole. This definition coincides with the most general definition of a system as a set of components or objects and relations among them. Systems theory is then the study of organisation and behaviour per se and a natural conclusion is therefore to consider systems biology as the application of systems theory to genomics.

b/ Winther RG. Systemic darwinism. Proc Natl Acad Sci U S A. 2008;105:11833. [PMC free article] [PubMed]

A significant amount of 21st century research focuses on systems (e.g., genomic, cellular, organismic, and ecological/global). Systemic Darwinism is emerging in this context. It follows a ‘‘compositional paradigm’’ according to which complex systems and their hierarchical networks of parts are the focus of biological investigation. Through the investigation of systems, Systemic Darwinism promises to reintegrate each dimension of Darwin’s original logical space. Moreover, this ideally and potentially unified theory of biological ontology coordinates and integrates a plurality of mathematical biological theories (e.g., self-organization/structure, cladistics/history, and evolutionary genetics/function). Integrative Systemic Darwinism requires communal articulation from a plurality of perspectives. Although it is more general than these, it draws on previous advances in Systems Theory, Systems Biology, and Hierarchy Theory.

These are: i/ the "systemic approach" I am talking of, ii/ the "dynamism" of a phenome and iii/ the "static" characteristic of the phenotype.

Notes:

i/ The systemic approach is relatively new only in medicine. The system theory is well known in philosophy, cybernetics, automatics etc. since 1950s.

ii/ I strongly think this aspect must be presented in the description of the phenome.--Gillcv (talk) 10:41, 4 October 2011 (UTC)

Phenome as a specific area of study

Hello, I don't want to reignite what was obviously a very heated debate as to whether phenome was an individual "thing" or a synonym of phenotype, but I work for the MRC-NIHR National Phenome Centre which opened in 2013 and the question we most often get asked is "what is a phenome"? We have some descriptions which we use to explain to both expert and lay audiences and also our Director has published some articles on it explaining the use of a person's phenome as a useful tool in patient and population stratification. I am happy to have a go and edit the page, but do not want to do so if 1. people feel there is a conflict of interest here and 2. it will cause massive issues. Advice/comments gratefully received please. DancingBal (talk) 15:51, 13 November 2014 (UTC)

• Personally, I think that "phenome" is a fashionable term (in this era of "omics") for something that doesn't exist or, at best, is an awkward synonym of phenotype. What people talking about "phenome" fail to understand is that "phenotype" is not necessarily univariate and may encompass many different characteristics of an individual and that if one would mean the collective phenotypes of groups of individuals or species, we already have terms like "norm of reaction" and such. But I start feeling like I'm fighting windmills here, as hardly anybody is interested in these old-fashioned notions (anything older than 10 years is outdated, right?) --Randykitty (talk) 20:12, 13 November 2014 (UTC)

Thank you for your comments Randykitty. The way I think about phenome, I believe, takes into account the fact that phenotypes are not univariate. I use phenome in the way that each individual is affected by the interaction between their genes and their environment. This way we can use the study of the phenome to stratify patients or the population in to risk i.e. it gives us the ability to look at why when looking at two people with the same genetic mutation which increases risk for a type of cancer, only one may develop cancer. I believe the phenome, in the way I understand it, gives us the ability to begin to look at the interaction of this wider environment with the genes of a person. This is not a flight of fancy, there are a large number of studies now looking at the effect of nutrition on cancer patients as previously developments of new treatments have been hampered by unknown reasons why the same drug does not work as well in different people - one of the main causes which has not been investigated thus far but which is increasingly being recognised as a significant effect upon such treatments and trials, is the nutrition of the patients (the effects of which can start to be unraveled by understanding the phenome via the use of metabolite analysis techniques. Thus I believe that the closer study and understanding of the phenome is a significant next step in understanding disease and population risk and will help researchers understand why simply genotyping a patient will never be enough to give the whole story. DancingBal (talk) 10:38, 14 November 2014 (UTC)

I'm sorry, DancingBal, but your response just illustrates what I am trying to say. If your replace "phenome" in the above paragraph with "phenotype", the meaning would not change. In addition, I suspect that you actually are not interested in either phenome or phenotype at all, but in genotype*environment interactions and/or epigenetics. Nobody, as far as I know, has come up with a sensible definition of "phenome" or been able to explain how this concept differs from "phenotype". --Randykitty (talk) 06:26, 19 November 2014 (UTC)

Have to agree with Randkitty 100% here.