Wednesday, April 30, 2014

NSF asks for comments on "genomes-phenomes" program; here's a comment - phenome is a silly #badomics term

Hmm.  Just got this in the emails.
BIO seeks community input on Genomes-Phenomes research frontiersJohn Wingfield, Assistant Director of the National Science Foundation Directorate for Biological Sciences (BIO), is pleased to announce the posting of a Wiki to seek community input on the grand challenge of understanding the complex relationship between genomes and phenomes.  The Wiki is intended to facilitate discussion among researchers in diverse disciplines that intersect with biology, such as computation, mathematics, engineering, physics, and chemistry.The Wiki format encourages open communication, captures new viewpoints, and promotes free exchange of ideas about the bottlenecks that impede progress on the genomes-phenomes grand challenge and approaches or strategies to overcome these challenges. Information provided through the Wiki will help inform BIO's future research investments and activities relevant to understanding genomes-phenomes relationships.To provide comments, ask questions and view input from and interact with other community members, first-time users should sign up for an account via this link:Sign-up.  Once registered, users will be directed to the main page of the NSF Wiki to accept the terms and conditions before proceeding.  Additional guidance and subsequent visits can be accessed via this link: Genomes-Phenomes Wiki.Community members should feel free to forward notice of this to anyone they think might be interested in contributing to the discussion. Questions regarding the Wiki should be sent to bio-gen-phen@nsf.gov.
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Nice that they are seeking input. But really - does NSF have to adopt "phenome" as a term? How exactly is this different from "phenotype"? This seems to be a case of exactly what I was criticizing in my Badomics article in Gigascience and in all my posts here (eg bad omics words of the day, Worst New Omics Word Award, badomics, etc). Blech. Genomics is really interesting. I have worked on it for many years. But there is no need to contaminate the literature by using new, uninformative, oversold terms like "phenome".

6 comments:

  1. How is genome different from genotype? I propose a 1:1 mapping of genotyping to phenotyping. Genes, phenes. Genotype, phenotype (the individual level). Genome, phenome (species level). Simple. We need better language to understand the physical manifestation of organisms that doesn't use generic, non-technical terms like trait or attribute that are used ambiguously at multiple levels of biological organization. People who are phenotyping and studying how trait variation affects function are having problems due to the lack of a conceptual framework to advance their field. Researchers in a gene first program may not realize that.

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    1. Interesting. Though I don't really agree. Genome is a term that has been used for a long time. So has phenotype. Why change now? The answer I think is simple - genomics is "hot" and people at trying to make other areas seem hot too. But that is not needed. Phenotype as a term works just fine.

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    2. Hi Jonathan,

      I just read your badomics paper and it actually clarified how genome was different than genotype, though I see genome used at the species-level, as well. I think you can take -omics too far, but gene-phene have been related since the beginning and there are reasons we have similar words like genotype and phenotype. Phene was used as early as 1925 in place of trait in genetic research, only 16 years after gene was coined. There is a natural relationship beene gene and phene that would better be exploited. Both research programs contain ambiguity besides, like people talking about a 'gay' gene instead of 'gay' allele (just an example). In phenotyping we have the same problem, with trait used as both general trait (hair color) and as attribute (brown hair).

      I published my ideas on these relationships here, and don't think they're limited to my own field of root biology at all:
      http://journal.frontiersin.org/Journal/10.3389/fpls.2013.00355/abstract

      I don't mean to plug myself, but rather to demonstrate that if we are trying to tackle more complex problems like how traits interact you can see how we are limited by ambiguity and lack of clarity in our language. In trait-based research we don't just need new words like phenomics, but many new ways to express ourselves more clearly and precisely. However, while phenome might be similar to phenotype in general use, phenomics has no corollary already in use as far as I know and is a useful term. Phenotypology? Nah. Functional phenomics just has a nice ring IMO :)

      Regards,

      Larry

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  2. Actually, according to Wikipedia, "phenome" is a surprisingly old term and not a "me-too" omics coinage like I thought. Apparently it was used as early as 1949!

    But yeah, at a personal level I dislike the term -- maybe because whenever I see the word "phenome" I think "pheromone".

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    1. Thanks for pointing that out Jonathan. Today I saw a talk where a person used phenotype as a particular state of a trait. Confusing.

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    2. Indeed, the OED has it from 1949 and the Google ngram view has it more common than genome until the 1940s

      https://books.google.com/ngrams/graph?content=genome%2Cphenome&year_start=1800&year_end=2000&corpus=15&smoothing=3&share=&direct_url=t1%3B%2Cgenome%3B%2Cc0%3B.t1%3B%2Cphenome%3B%2Cc0

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