tlemberger omics mania: 'ethomics' http://is.gd/wOcg - should be added to http://omics.org/ but perhaps also nominated for this http://is.gd/g2Bc
That is from Thomas Lemberger and so I followed the last link first, since I thought I might be to, well me. And indeed it was a link to my "Worst new omics word award" for museumomics.
And so then I went to the link on ethomics: High-throughput ethomics in large groups of : Drosophila : Abstract : Nature Methods.
And indeed they use "ethomics" - what is clearly a quite new omics word (only 62 google hits as of this PM). I confess, I stopped reading at the abstract because it was just too much:
We present a camera-based method for automatically quantifying the individual and social behaviors of fruit flies, Drosophila melanogaster, interacting in a planar arena. Our system includes machine-vision algorithms that accurately track many individuals without swapping identities and classification algorithms that detect behaviors. The data may be represented as an ethogram that plots the time course of behaviors exhibited by each fly or as a vector that concisely captures the statistical properties of all behaviors displayed in a given period. We found that behavioral differences between individuals were consistent over time and were sufficient to accurately predict gender and genotype. In addition, we found that the relative positions of flies during social interactions vary according to gender, genotype and social environment. We expect that our software, which permits high-throughput screening, will complement existing molecular methods available in Drosophila, facilitating new investigations into the genetic and cellular basis of behavior.
For trying to extend omics to ethogram and beahvioral plots I am giving my second coveted "worst new omics word award" to Kristin Branson, Alice A Robie, John Bender, Pietro Perona & Michael H Dickinson. Here is a prediction - ethomics will not become widely used - not soon - not ever. Thanks for pointing this one out Thomas.
i know its an oldie (which i unabashedly stole from dean.snow...), but, my favorite -omics is the study of the relationships of young women with groups of elderly and kindly, if smallish, men having unique personality types.ReplyDelete
wait for it ...
I think it is now time to call in the Dept. of ome-land security.ReplyDelete
(ba dum bum, cymbal crash)
All you two have to do is get one of those in a paper and you might get an award ...ReplyDelete
The sad thing is, this is really cool stuff. I saw Dickinson talk about it at the Fly Meeting this year. He's got some awesome videos and clever ways of representing the data. Too bad they spoiled it with a lame name.ReplyDelete
May not have been their idea to call this ethomics. My own contribution to the omics word game (phylogenomics) was only coined b/c the editors of a commentary paper wanted us to give what we were doing a name ...ReplyDelete
I received a comment recently that the Blogger system seems to crack on and will not publish. So I am posting it here myself in two parts as it seems the problem is the length of the comment:ReplyDelete
Part 1 from Michael Dickinson:
As a senior author on the paper in question (‘High-throughput ethomics in large groups of Drosophila’), I though it would be useful to provide my input in this discussion.
First, let me set the record on the evolution and usage of the work ‘ethomics’, which we used in our title. As far as I know, the term was originated by me, although as with any new term it may have occurred independently to different people and I stake no special claim to its use. I began using the term a year or two ago when giving lectures on new methods for objectively quantifying behavior in genetic model organisms, particularly Drosophila. The development of such methods (based mainly on new advances in machine vision) for quantifying behavior is the goal of a joint research project with Pietro Perona, a colleague at Caltech. The methods that we have developed so far are the brain child of Kristin Branson, a post-doc working on the project, with the help of Alice Robie, a graduate student. During research seminars, I began describing such methods as either ‘ethometrics’ or ‘ethomics’. I all honesty, I started using the latter term primarily to get a laugh. I think most people find it amusing because of the rapid proliferation of ‘omic’ terminology and because the idea of high-throughput, quantitative analyses of such a fuzzy high-level phenotype as behavior is a bit absurd. When my co-authors and I were brainstorming for a title of the manuscript we (as is often typical when choosing titles) struggled with various versions until one of us blurted out a title using ‘ethomics’. As we could not think of anything better the name just stuck. In full honesty, I think we imagined that the title would probably be rejected by editors or reviewers but it would serve as a decent place-holder in the meantime. As it was, no one complained and the title stood. My motivation here is not to deflect criticism - as a senior author I take responsibility for any errors in the manuscript – but rather to set the record straight on the initial formulation and use of the term which some find so objectionable.
Part 2 of the comment from Michael DickinsonReplyDelete
As noted above, I accept any criticism for the use of an objectionable term and certainly respect the opinions of my peers regarding the proliferation of unnecessary jargon. I am, however, concerned with the tone of the discourse on this and other blogs, which I do not think stimulates productive discourse of important scientific issues. The original note objecting to the use of the term ‘ethomics’ was accompanied by the following statement, ‘I confess, I stopped reading at the abstract because it was just too much’. Dr. Eisen, who is clearly an accomplished and thoughtful scientist, was nevertheless willing to render judgment on a new approach based solely on his reaction to the title – without even taking the time to read the abstract, not to mention the rest of the paper. Perhaps our use of the term ‘ethomics’ is objectionable, but I would think that such opinion should depend on the details of the methodology as described in the manuscript. Briefly, the motivation behind our project is that we believe the methods for manipulating the genotypes of genetic model organisms are far outpacing the methods for objectively scoring the phenotypic consequences of such manipulations. This is particularly a problem for behavior – a phenotype that is extremely difficult to define or measure quickly or objectively. Thus, although some might think the use of the term ‘ethomics’ is a bit silly, our sincere intent – outlined within the manuscript - is to develop technology for measuring behavior that is at least coarsely analogous to the robotic sequencers that enabled to development of genomics. A high-throughput analysis of behavior is wrought with severe difficulties, and will never achieve the automation of genomic sequencing. However, I believe that the integration of genetics and behavior is impeded first and foremost with the difficulties in defining and measuring behavior and that the field must make a concerted effort to automate a field of science that is still performed primarily by direct observation or manually scoring recorded video sequences. I also feel that the dismissive tone of the prior blog entries is ironic, given Dr. Eisen’s admirable dedication to open source publication. A clearly-stated objective of the manuscript in question is to provide the Drosophila community with freely available open source tools. In the past, several laboratories (including my own) have developed technology for quantifying behavior that was too complicated or too finicky to disseminate through the research community as easily as the molecular and genetic methods with which it must keep pace.
Our effort, and others like it, may represent baby steps and perhaps the term ‘ethomics’ is not warranted, but to dismiss an approach without making the effort to even read the abstract does not seem to me a productive way at initiating a discussion on an important topic.
My final thoughts relate to the nature of scientific blogs, their promise, and the sort of culture that they promote. I strongly commend Dr. Eisen on his efforts in providing the public with a source of information on many critical topics. I believe, however, that there is something about the nature of blogs – perhaps the lack of formality derived from email etiquette – that fosters a less-than-civil tone that is not productive for stimulating thoughtful discourse. If a scientist visited a poster at a meeting, presented by graduate students, would he/she say to them, ‘I thought your title was stupid so I did not bother to read your abstract’? Yet the comments of a blog are posted instantly for all to see, not just the senior authors who should take the heat of criticism, but all the graduate students, post-docs, and undergraduates who contributed to the research. Having read various blogs, it seems to me that quick ‘snarky’ comments accrue some currency, such that discourse can be more about wit than about substance. My wife, who is a science journalist, has suggested that perhaps this culture arose from the fact that many scientist bloggers spend much of their time dueling with creationists or climate change doubters, which immediately establishes a contradictory tone that bleeds into discussions of less adversarial topics. There may be no single explanation, but I do believe that bloggers need to be more thoughtful about the comments they post. I obviously cannot know for sure, but I imagine that if I had a face-to-face discussion with Dr. Eisen on the topic of molecular genetics and behavior that we would have a stimulating discussion, free of derogatory comments. Should not such conversation be the goal of web-based discourse?
Thanks for the input and your comments. I accept your criticisms and apologize for the offense. However, I am still not sure where I stand on "snarky" vs other forms of discussion of science.
One of the goals of my blog has been to try and make it similar to what scientists say in private about science. The culture of science without a doubt includes humor, alas, sometimes at the expense of others (consider, for example, the IgNobel prizes, which I think do wonders for science in that they show a more lighthearted side of science).
Thus we could ask, as you do, would I use this tone at a poster discussion? Possibly. But certainly if I saw you give a talk and you used the term "ethomics" I would groan. I do find it a bit ironic that you may have used the term to get a laugh but that you may be uncomfortable when others make light of it too.
However, certainly it would be bad to say at a poster that "I think your title is stupid and therefore I am not going to talk about your work." And that is the impression given my my comment about not reading more than the abstract. Alas, that was lame and lazy attempt by me to make a comment about open access as I did not have access to your paper when I was writhing this and could not read any more than the abstract (and cannot do so now either). Sometimes I get tired of making my pro open access comments and here I got lazy and clearly it implied the wrong thing.
So in the end - I think you are right I could have made a more useful contribution to the field by discussing your work and not just your word (which I still do not like ...). And certainly my comment about not going past the abstract was not helpful and I should have just said as I usually do "I cannot read more than the abstract b/c I do not have access from where I am." I will try to do better next time I try to insert humor into the discourse among scientists.
does the omicome really need analysis?ReplyDelete