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May 5, 2012 5:37 PM   Subscribe

Omes have a long history and describe general interactions of biological information objects in various omes. But not all omes are real omes. Some have a problem with omes as neologisms.
posted by Blazecock Pileon (31 comments total) 7 users marked this as a favorite

 
Is this a real thing or is it some sort of SEO thing? The third link makes it look like it's connected to domain name speculators.
posted by XMLicious at 6:05 PM on May 5, 2012


So omes are the future.

But I find it a little ominous that economics is the environmental omics for all the omes. I was sort of hoping we'd get past that particular rationalism.
posted by de at 6:07 PM on May 5, 2012


The third link makes it look like it's connected to domain name speculators.

You're totally right: I've been in league with domain name speculators for the last six years, but I've waited until now to let the cat out of the bag.
posted by Blazecock Pileon at 6:09 PM on May 5, 2012 [2 favorites]


No, I'm not saying it's a self-link, I'm saying that a bunch of the domain names in the third link go to similar vanilla wikis.
posted by XMLicious at 6:11 PM on May 5, 2012


(the ones I clicked on, at least.)
posted by XMLicious at 6:11 PM on May 5, 2012


Like, take a look at vaccinomics.org
posted by XMLicious at 6:15 PM on May 5, 2012


XMLicious, it seems mostly legit, if sparse. The spammers probably got to some of them, since they are, after all, wikis. *omics is definitely a real trend in the biosciences over the last decade or so (e.g.), though some of the latest coinages are definitely eye-rollers (hygeinome?! really??).

Was this at all inspired by this NYT article?
posted by en forme de poire at 6:34 PM on May 5, 2012


definitely definitely, definitely
posted by en forme de poire at 6:34 PM on May 5, 2012


Quoted from the last link for truth,

"It is an old maxim that if you want to get on, invent a new word for your particular niche in an old area, and so become an instant expert. This process seems to have gone mad. A recent article in The Scientist that referred to "nutri genomics" 1 prompted me to see just how many -omics had now been coined. Well over 100 neologisms are listed at [http://www.genomicglossaries.com/content/omes.asp]. A few of the more ghastly examples are foldomics, functomics, GPCRomics, inomics, ionomics, interactomics, ligandomics, localizomics, pharmacomethylomics and separomics. None of these refers to areas of work that did not exist before the coining of the new word. Perhaps, as an electrophysiologist working on recombinant ion channels, I should dub myself an expert on ohmomics. This habit of coining fancy words for old ideas might be thought harmless, merely a source of endless mirth for thinking scientists. I'm not so sure though. Apart from reinforcing the view of scientists as philistine illiterates (at least when it comes to etymology), actual harm is done to science as the public becomes aware that some among us seem to prefer long words to clarity of thought." (PDF)

I lost my shit at ohmomics, hilarious.

A lot of this seems to stem from the fact that science journalists seem incapable of understanding much less communicating anything in biology past the early 1960s or so as anything other than absolutely new. Most of the discoveries since then are new to them, and new to their reader, and so it is almost like they feel like they can get away with it. They don't seem to be wrong.

I was once in a crowded airport van full of intelligent, engaged, and educated people all listening to the radio, I think it was an NPR affiliate, which was sparking good conversation. There was this story that came on about a researcher who had done some really cool work with DNA polymerase that had some really exciting prospects for drug development, but I could only barely discern that from the story. The journalist interviewing the poor guy only managed to get to a point where it became necessary to understand PCR to continue, and then proceeded to somehow get the idea that he had invented PCR for the work he was being interviewed for.

I was horrified, this was such a colossal embarrassing failure on the part of the journalist's, and the trainwreck just kept coming. It was a 20 minute story breathlessly reporting the new invention of PCR, then more than 25 years old. PCR is absolutely central to the great majority of all of the great discoveries and mundanely necessary understandings of the last 30 years of biology, and not only was this program failing to understand its impact and butchering the concept, but no one in this van would have known the difference.

Even the omes and omics that make sense like proteomics and transcriptomics were generating Nobel prizes half a century ago, they really are new words for very old concepts. In general I find the trend annoying and shallow, it devalues and hides old work that is already way to fucking hidden, it rewards deuchebags with slick tongues and access to rubes but little to contribute to these old disciplines, and it doesn't actually contribute anything.
posted by Blasdelb at 6:38 PM on May 5, 2012 [6 favorites]


TimeCubeOmics.
posted by charlie don't surf at 6:47 PM on May 5, 2012


I was up all night studying yourmomics.
posted by horsewithnoname at 6:55 PM on May 5, 2012 [8 favorites]


The spammers probably got to some of them, since they are, after all, wikis.

Well note that they're wikis that can't be edited anonymously, at least currently, nor can you self-register an account without approval. And the "BioLicense" link that appears at the bottom of all of these sites (which makes it seem even more certain that the domain registrations have something in common) goes to yet another plain vanilla wiki.

But if it's a legit topic in general, carry on.
posted by XMLicious at 6:57 PM on May 5, 2012


So who lives in omes? Omies?

I am so, so sorry
posted by Halloween Jack at 7:30 PM on May 5, 2012 [1 favorite]




It's riding on the coattails of the two big omes -

The Genome - which, after exhausting effort, has been completely mapped for humans. We have no idea what it means, because all those genes are instructions that create other, more complex instructions. Which brings us to...

The Proteome - This is the big one. It's how proteins form from genetic material into complex organic structures. It's what "F@H" is trying to compute... how life itself comes into being from base principals. You map that, you map how a living organism comes to be, and you conquer frontiers of medicine and biotech we can't even imagine. Biosingularity.

Since the Genome and Proteome gets all the grant money, other 'omes" come into being to hitch their wagon to that shooting star, to gather grant-money from idiot donors. It's kind of seedy and unseemly, you ask me.
posted by Slap*Happy at 8:01 PM on May 5, 2012


The omics links are all dead. Awesome.
posted by Joseph Gurl at 8:14 PM on May 5, 2012


The omics links are all dead.

Massive failure of the linkome.
posted by Rock Steady at 8:40 PM on May 5, 2012 [6 favorites]


I must be on the frontier of linkomics, because they're still working for me.
posted by Blasdelb at 9:40 PM on May 5, 2012


Then there's the study of not propagating the genome: onanomics.
posted by michaelh at 11:04 PM on May 5, 2012


I heard some guy on the radio ranting about Obama-omics.

I also heard somewhere that in Iceland they are studying the problems of a community of small people abandoning their countryside culture and moving to the city and becoming hiptsers: Metrognomes (okay it's late and I'm tired).
posted by eye of newt at 12:28 AM on May 6, 2012


I expect this thread to produce significant contributions to snarkomics
posted by Dr Dracator at 3:10 AM on May 6, 2012


Everyone knows omes are really hard to control.
posted by oulipian at 4:02 AM on May 6, 2012


OMEMG WTF?
posted by Decani at 4:50 AM on May 6, 2012


The linked "omics" site seems like pure marketing bullshit: "Omics is a progressive and useful concept in biology. It can revolutionize the way biology is done and how we see life in the future." Wow, I'll take two!

> A lot of this seems to stem from the fact that science journalists seem incapable of understanding much less communicating anything in biology past the early 1960s or so as anything other than absolutely new.

You could have deleted everything after "anything."
posted by languagehat at 8:03 AM on May 6, 2012 [2 favorites]


The linked "omics" site seems like pure marketing bullshit: "Omics is a progressive and useful concept in biology. It can revolutionize the way biology is done and how we see life in the future." Wow, I'll take two!

Be sure that they're genomics and proteomics. There is, I think, a useful distinction between "studying an X (in relation to Y)" and "studying the collection of X's in parallel (and their group relationships to Y)". -omics are often about the technology and analytical methods of doing what would have been a single study 10-20k times and trying to take advantage of information one gets by doing them all together, like network structure in genomics.

(I just had to add genomics and proteomics to my spellcheck dictionary.)
posted by a robot made out of meat at 12:18 PM on May 6, 2012 [1 favorite]


To be sure, some of the endless *omics proliferation is pure marketing fluff, but neither is the term totally content-free. I think a robot made out of meat has the right take. Used as a suffix, X-omics mostly refers to studying a lot or nearly all of the Xs in parallel, as opposed to one or two at a time. As I understand it, the original "ome" was the genome, which was coined nearly a century ago; post-genome-sequencing, though, "genomics" came to mean an approach involving measurements of nearly all the genes in the genome. "Proteomics", transcriptomics, and "metabolomics" are more recent coinages (back-formations?) that extend that concept to proteins, gene transcripts, and metabolites, respectively. As Blasdelb points out, this isn't to say that nobody was doing genomics or proteomics or even metabolomics in the 70s, but the sillier cases aside I do think it fills a useful gap in the language.
posted by en forme de poire at 7:34 PM on May 6, 2012 [1 favorite]


The Proteome - This is the big one. It's how proteins form from genetic material into complex organic structures. It's what "F@H" is trying to compute... how life itself comes into being from base principals.

Incidentally, this is more a description of the protein folding problem (or "foldomics", har har). Proteomics is more the study of how to measure which proteins and how much of them are being made.

We have no idea what [the genome] means, because all those genes are instructions that create other, more complex instructions. Which brings us to... [...] The Proteome

From using things like sequence analysis (e.g., what genes is this similar to in other organisms?) and transcriptomics (e.g., when and where is this gene made?), we actually have a decent idea of what many genes in the genome do. Our understanding is pretty severely lacking in how these genes work together, though. And a lot of the most mysterious parts of the genome (e.g. lincRNAs) regulate genes without ever being made into proteins themselves.

I definitely believe computational predictions of protein folding are going to get a ton better over the next few decades -- but even with a perfect understanding of protein structure we would still be way, way off from being able to simulate what goes on inside a cell via something like molecular dynamics. A typical cell has thousands of proteins; cutting a lot of corners, we can barely simulate a pair of proteins (or a protein plus a much smaller molecule, like a drug), and even then it's only possible to run the simulation for around a microsecond of "real time." Going beyond that, each cell in the human body produces a different cohort of transcripts and proteins, and on top of that cells are constantly getting inputs from each other (neuronal, endocrine, etc). So I think it's going to be a very long time before MD really bears that kind of fruit.

That said, there's no shortage of experimental and computational approaches we can use in the meantime.
posted by en forme de poire at 8:08 PM on May 6, 2012


Transcriptomics makes some sense1, and foldomics is really pushing it, but metabolomics? Really?

I get that genomics has been hyped to a public that barely understands what a gene is, and so other fields that are necessary for genomics-as-hyped need access to that fame, but metabolomics doesn't even make sense. Metabolites have such a bare and convoluted conceptual relationship to chromosomes, or what they do, that this is just ridiculous.

1I'm about to start a project for which transcriptomics is actually a pretty good descriptor, and I intend to use it, but it still makes me really uncomfortable. I'm incredibly grateful to have been trained in the lab of someone who was doing old school genetics back in the day who exposed me to a lot of the amazing work that people did back then. Because it is in many ways much better than anything I'd have the patience for and is being quickly forgotten as the old guard is slowly less able to come to conferences and Elsevier strangles us away from anything printed more than 10 years ago. I'll be using sequencing techniques that are many orders of magnitude fancier and need fancy programs to sift through the massive amounts of data it will generate, but the questions I'll be asking will be more or less similar.
posted by Blasdelb at 9:38 PM on May 6, 2012


(Full disclosure, some of what I do could be described as metabolomics.)

Blasdelb, you're right metabolomics doesn't have the same direct link to the genome that the transcriptome has, but I think the term makes sense nevertheless. In this case, the "-omics" suffix refers to the attempt to quantify all metabolites, or as many as possible, in an analogy with transcriptomics involving the measurement of all transcripts, or proteomics involving the measurement of all proteins.

Metabolomics is actually one of the more mature of the "omics"es - the term dates back to at least 1998, which seems to be roughly contemporaneous with the first uses of "proteome" and "transcriptome" (around 1995).

I agree that the list in the wiki is ridiculous. I really wish there were a list of Pubmed hits for each of the "omes" -- on a first look a lot of them have zero. Of the ones I've actually heard used (by more than one person and non-ironically), the breakdown goes like this:
  1. Genome: 799,963
  2. Proteome: 21,381
  3. Transcriptome: 10,157
  4. Metabolome: 2,226
  5. Microbiome: 2,179
  6. Interactome: 980
  7. Epigenome: 842
  8. Exome: 618
  9. Kinome: 370
  10. Phenome: 183
  11. Foldome: 1 Okay, I have never heard anyone use "foldome" in a non-facetious way, I just thought it was funny that there was exactly one paper on it. Also, I'm using a lot of quotation marks in this thread. Blasdelb: you using BOWTIE?
posted by en forme de poire at 12:14 AM on May 7, 2012 [1 favorite]


...repeating that for "*ome OR *omics":
  1. Genome: 843,278
  2. Proteome: 44,605
  3. Transcriptome: 11,363
  4. Metabolome: 5,256
  5. Microbiome: 2,182
  6. Epigenome: 2,068
  7. Interactome: 1,054
  8. Exome: 618
  9. Kinome: 386
  10. Phenome: 334
  11. Foldome: still just 1
posted by en forme de poire at 12:23 AM on May 7, 2012 [1 favorite]


So, are there any truly bona omes?
posted by MartinWisse at 5:26 AM on May 9, 2012


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