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.

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”.

#Badomics word of the year already? Yup. The ‘Consciousome’ from Deepak Chopra

Oh my.  As many out there know I have a thing with “badomics” words.  These are words someone has invented where they have added the ome suffix on to the word to try and capture some of the hype of genomics.  And though many many people do this, the ones I call “badomics” words are the ones where the ome addition is all hype and no use.  And this AM I was informed of a doozy via Twitter:

And so I went to the link and found this: Self-Directed Biological Transformation Initiative — A New Frontier ‘Consciousome’ | Deepak Chopra and Rudolf E. Tanzi.  And what I found there was almost a textbook example of how to create a badomics word.  Here is the critical paragraph

The current frontier in brain research, to map the entire connectivity of the brain, the so-called connectome project, points to an even more exciting frontier, the “consciousome.” This takes the brain to the next level, where we need to explore how our conscious choices may liberate us from biology-as-destiny. Our conscious choices and reactions to life experiences remodel the neural circuitry of our brains and, now, we need to explore the effects on our genomes.

Just what is the consciousome?  I cannot tell.  But it has something to do with genomics.  And with consciousness.  Hmm.  They try to clarify later on

Where the connectome is like a diagram of all the telephone wiring in a city, the consciousome embraces the conversations taking place using the wiring.

Not really helping.  So – what does it have to do with genomics?  Unclear until later

By opening up the genetic doorway to consciousness, however, we take a leap forward. For example, recent studies indicate that meditation can have a strong effect on the length of chromosome telomeres, the nucleotide sequences that protect chromosomes from the deterioration linked to aging. That these beneficial effects occur immediately indicates just how responsive genetic activity is to mind-body interventions — something never previously suspected.

So – the consciousome is the affect of conscious thought on the genome?  Whether or not you think this is something worth studying, the slapping on of the ome term on the end of consciousness is a self directed thought that should never have been done.  There is no entity that is the consciousome.  The term makes no sense.  It is certainly a badomics word of grand magnificence.

I note – there is some seriously bizarre other stuff in this article like the following:

In our Self-Directed Biological Transformation Initiative, a 100-subject study to map biological transformation, leaders in the fields of healthcare, art, business, environment, sports, entertainment, science and technology will be given a protocol to measure new genetic activity, searching for positive evolutionary effects

What?  How exactly are they searching for “positive evolutionary effects” and what does that even mean?  And why do this with the “leaders in the fields …”. How are they supposed to be different?

And also

This “soft inheritance,” in which the parents’ life experiences and behavior may directly influence the genome of their offspring (transmitted via the epigenome), is arguably the most profound “living legacy” we can pass along to our children.

So now they have gone from a few studies in mice showing epigenetic inheritance of a few things to the “most profound living legacy we can pass along to our children”.  Uggh.  Talk about overselling genomics – this is overselling a word / field that does not even exist yet and the word certainly should not exist ever.  Personally, I think brain science is very very interesting and important.  Let’s not cloud it up by coining new fuzzy terms, trying to capture the hype of genomics, and overselling the science.  And for this, Deepak Chopra, Rudolf Tanzi and their coauthors Tara Sheahan, Gina Murdock, and
Glenda Greenwald are winners of the coveted “Worst New Omics word award.”

Bad Ome-like word of the week: symbiome

Well I got pointed to this paper: Transgenerational Transmission of the Glossina pallidipes Hytrosavirus Depends on the Presence of a Functional Symbiome

And as many might guess – the word “symbiome” did not sit well with me.  Alas, they don’t define it in the paper.  So I can’t really quibble with their definition.  But I did find some other stuff out there that, well, at least helps see how other people are using the word:

I can’t really tell from most of these if “symbiome” can be a useful term or not sometimes.  Certainly the iPhylo example above has potential.  But in general, the word seems awkward at best.  Now – as far as I can tell, nobody is using it in the context of “genomics” so this does not fit in with my “badomics” obsession.  But it still does not make me feel warm and fuzzy so I am going to give it a pseudo-award – the Bad Ome-like word award.

Badomics word of the year? Nutrimetabonomics

So I guess a thank you is owed to Joseph McPhee for this tweet:

The link in the tweet is to this paper.

Nutrimetabonomics: Applications for Nutritional Sciences, with Specific Reference to Gut Microbial Interactions – Annual Review of Food Science and Technology, 4(1):

Wow. Nutrimetabonomics.  In a paper.  And amazingly they had a conference on this too. 11th-13th April 2012- First Nutrimetabonomics Workshop to consider …  I do not even know what to say.  This is NOT a good omics word.  It is definitely a bad bad bad omics word.  A very bad one (note – the field might be interesting .. the word however is bad).

For more on #Badomics words see

#Badomics word of the day, week and month: the morphome

Well, I have been avoiding the badomics meme for a little bit but cannot help getting back into it for this one.  From this paper: BMC Biology | Full text | The songbird syrinx morphome: a three-dimensional, high-resolution, interactive morphological map of the zebra finch vocal organ.  Yes, that is right – rolls right off the tongue – the songbird syrinx morphome.

The key sentence assigning guilt for this

“Here we present an annotated high-resolution three-dimensional (3D) morphological dataset, which we have dubbed a morphome,”

Note – I love the move for more high throughput, digital morphological data.  It rocks.  It will make for some interesting science.  It however, does not deserve it’s own ome word.

For more on this meme see All my writings on badomics words.

H/T David Coil …

A badomics word for good purposes: new paper on the "ridiculome"

Quick post here.  There is a new paper in BMC Biology which uses a bad omics word in the paper and in the title: BMC Biology | Full text | Logic modeling and the ridiculome under the rug.  Fortunately they are using the term to poke a bit of fun at people who think genomics will solve all of their research problems.

Referring to 16S surveys as "metagenomics" is misleading and annoying #badomics #OmicMimicry

Aargh.  I am a big fan if of ribosomal RNA based surveys of microbial diversity.  Been doing them for 20+ years and still continue to – even though I have moved on to more genomic/metagenomic based studies.  But it drives me crazy to see rRNA surveys now being called “metagenomics”.

Here are some examples of cases where rRNA surveys are referred to as metagenomics:

I found these examples in about five minutes of googling.  I am sure there are many many more.  
Why does this drive me crazy?  Because rRNA surveys focus on a single gene.  They are not gnomicy in any way.  Thus it is misleading to refer to rRNA surveys as “metagenomics”.  Why do people do this?  I think it is pretty simple.  Genomics and metagenomics are “hot” topics.  To call what one is doing “metagenomics” makes it sound special.  Well, just like adding an “omic” suffix does not make ones work genomics – falsely labeling work as some kind of “omics” also does not make it genomics.
Enough of this.  If you are doing rRNA surveys of microbial communities – great – I love them.  But do not refer to this work as metagenomics.  If you do, you are being misleading, either accidentally or on purpose.    So I think I need a new category of #badomics – “Omic Mimicry” or something like that …
Note – this post was spurred on by a Twitter conversation – which is captured below (note – I am certain I have complained about this before but cannot find a record of it …)






#Badomics word of the day & Worst New Omics Word Award: CircadiOmics

Really?  We need this new omics word in this paper?: CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics : Nature Methods : Nature Publishing Group

The good news?  I can’t actually get the full text of the paper right now so I can’t read what they say about this word.  The bad news?  A lot.  First, the definition is in the title.  And it is pretty clearly a badomics word.  Also, they seem to be serious that other people should use this word without laughing.  There is a website: http://circadiomics.igb.uci.edu.  Uggh.  This is an unnecessary addition to the biology lexicon.  Why not just saw “genomics of circadian rhythms”?  Does this really need a new word?  I don’t think so.  So I am giving these authors my “Worst new omics word award” though I am not 100% sure how new the word is ..

For more on #badomics words see also::

Trying to track down source of cartoon about coining "ome" words #badomics

I have this cartoon of direct relevance to my crusade to end the use of badomics words.  I have been trying to track where it came from for – like – ever.  And though I did not want to post it without getting permission I have decided to do so to try and track it’s source.  Here it is

I note – I tried using Google Image search (see a discussion of how to do this here) and it finds some other versions of this cartoon online but none of them have a source for it either.  

So – does anyone out there know where this came from?