I was chatting with Richard the other day about his pet protein ZRANB2. Something about the name rang a bell, and sure enough I found that one of its orthologues was present in my own cell morphology screen. I was interested to see that we called the same gene ZNF265 instead, so Richard tootled around and discovered that this gene’s ‘official’ symbol was ZNF265 according to OMIM, but ZRANB2 according to NCBI Entrez and HGNC.
Sweeter than pancakes iHOP is one of several useful genomics resources
Most genes have a bewildering array of synonyms, of course, but in this day and age, you would hope that the genomics community would have settled on one unique one. In short, Richard and I shouldn’t have had to stop to disambiguate before delving into the really interesting questions, and this was the third such hitch I’d experienced in the past month. I’ve been using the superlative iHOP (Information Hyperlinked over Proteins) as my one-stop genomics shop (a site which, incidentally, falls firmly into the ZNF265 camp), so I emailed the person in charge, Robert Hoffman, to see if he could shed any light.
Robert, who turns out to be a lovely chap, told me that the HGNC is the ultimate authority; they curate and publish the latest names, and other organizations pick them up. “Of course,” he pointed out, “this does not mean that other people will understand you better if you use the official HGNC name, because many continue using the names the are used to.” So why didn’t iHOP call Richard’s gene by the HGNC appellation, ZRANB2? He confessed that this information is updated on iHOP only twice a year because it takes a long time for people to take up the trend, and meanwhile the NCBI ID number is more critical. NCBI, he notes, is quicker to respond to any changes in HGNC nomenclature.
So, I’ve duly bookmarked the HGNC website, but I still think there is a big problem out there. If any of you are in the gene discovery business, you’ll know that when you start getting interested in a new gene, it’s a nightmare to find a consensus nucleotide sequence in GenBank. I am not wholly innocent in this entire affair, as I single-handedly deposited about sixty different sequences for the feline leukemia virus envelope gene into GenBank during grad school, a veritable menagerie of subtle and esoteric polymorphisms. If you want to find out the common or garden FeLV env sequence in this mess, good luck to you. Associated with each gene name are not just polymorphic sequences, but truncations, splice variants, fusion proteins and the like. The FeLV community recognizes at least two ‘type species’ of the virus – FeLV-A/Glasgow and FeLV-61E – but this information is not, as far as I can see, linked to any of the GenBank entries. And it’s the same story for any gene you look up – which of the hundreds of entries, or sometimes thousands, is the ‘right’ one?
And the next step is even more disheartening. Looking up your new gene of interest in PubMed is not an easy way to grasp a coherent idea of what’s been published in the literature. Abstracts are littered with synonyms (and some pairs of different genes have the same synonym), but there is no unique gene identifier, as far as I can see, associated with the abstracts. I have no doubt that text miners are hard at work at this problem, but I haven’t seen anything helpful recently. And when you start being interested in homologues in other species, things start to get even murkier.
I realize that my gripes are probably naïve and possibly reflect ignorance of the state of play, but I suspect I am not alone. Maybe a good first step would be for journals to enforce the use of the NCBI ID number (or some other approved unique identifier) in all abstracts that mention a gene name, and for PubMed to add them retrospectively to their older abstracts.
Yes! And even if you used database identifiers instead of HGNC names you could run into trouble – in the abstract did you mean the gene as we knew it in 2000, or in 2002, after we discovered those extra exons? In the position it was in on the initial genome assembly, or a million basepairs further down in the latest version? The same gene in different contexts needs different identifiers (or at least version numbers), but you still need to be able to pull all that together somehow and pull out the information you need.
You do not want to get me started.
One of the transcripts that changes in my arrays has an innocuous sounding name. But it turns out that it’s a major splicing regulator when know by the name that people in the field call it. A hastily-scribbled PostIt note on the poster detracted from the gravitas, I feel.
And ZNF265/ZRANB2. Why can’t these things have meaningful names? (Because you haven’t worked out what it does yet — Ed) At least the original name told you it was a zinc finger protein. So does the new name — but implies it’s like a class of zinc fingers that have a known function. But that’s crazy talk, see, because we know that it can’t have a similar function as the RanBP proteins because, if nothing else, it binds RNA and not protein.
Naming proteins after their structure is madness. Structure doesn’t mean anything. Not at that level — as I keep telling all the people at this conference, yes it’s a zinc finger, no it doesn’t bind DNA: here, have a copy of my review.
I worked on something that was discovered and named almost simultaneously by a bunch of different labs. My lab calls it CNrasGEF, but it’s also known as… (let’s see how far I get without looking it up…) RAPGEF2, PDZ-GEF1, RA-GEF1 and (here is where I had to look it up) nRap-GEF1.
The official mesh term is RAPGEF2, but PDZ-GEF1 seems to be the most widely used. It’s a guanine-nucleotide exchange factor (GEF) and it activates both Rap1 and Ras, but Ras only in response to cyclic nucleotide (CN) activation. It also has a PDZ domain that turns out to be pretty useful for finding it’s way around the cell. So all the names make sense, but it would be much simpler if we all collectively called it “Phil” or “Fred” or “Lucy” or something.
I don’t know about Richard, but this is a subject concerning which you shouldn’t even begin to think of approaching me without due preparation, some propitiation, a few routines of extreme submission and a large bar of chocolate. Gee Dormiens Numquam Titillandus. If you think I get worked up about
DawkinsUnicycling Girrafes, you ain’t seen nothing yet, partly because it’s something that concerns me as the editor ofrealold-fashioned biology at Nature.Biological taxonomists have been doing this for years, nay, centuries, and there is now a rigorously enforced Code governing the nomenclature, synonymy and naming standards, so people do not get confused between, say, a raven, and
another slightly different ravenwriting desk, without the need for what Jenny so elegantly calls ‘disambiguation’.Yet it’s really, really hard to impress on biologists outside taxonomy how very important this is. Quite often they look at me rather indulgently as if I’m stuck in a Victorian time-warp, so unhip it’s a wonder my bum doesn’t fall off, a museum piece like all the things I study.
Well, they’re not laughing now, are they? Molecular biologists are getting into the same problems and making the same mistakes that were sorted out, in
real biologytaxonomy by Linnaeus, more than two hundred years ago. Now whose bums are falling off, eh?The Costa del Schadenfreude, yesterday
Henry – have you had to deal with many fungi? Some of them have two names, depending on which part of the life cycle they were in. You can imagine the fun.
I think eyespot researchers were quite relieved when someone found the teleomorph of Pseudocercosporella herpotrichoides and gave it a simpler name.
I was thinking wistfully about Linneaus when I wrote the post, as well as IUPAC, the draconian committee that keeps the chemists firmly in line.
Richard, I know what you mean about the hazards of naming proteins after their domains. I know a colleague who discovered that gene X bound to her gene of interest, but she immediately discarded X from her shortlist because – although s function was entirely unknown – the name implied it had a binding domain characteristic of a protein that she assumed wasn’t important for her biology. When I pointed out that the domain in question was just a short, promiscuous protein-protein binding domain which just meant that X bound to something else, and that the name implied nothing about what pathway it was actually in, she still didn’t want to know. The name had misled and poisoned her enthusiasm.
The power of naming things, eh?
I think eyespot researchers were quite relieved when someone found the teleomorph of Pseudocercosporella herpotrichoides and gave it a simpler name.
Those naughty fungi, eh? As you will imagine we get a few papers about the worldwide decline of amphibians and its relationship to the presence of the fungus Batrachochrytium dendrobatidis. There are all sorts of explanations for the mechanism whereby this organism kills frogs, but my favourite theory is that the poor things die when they try to spell its name (let alone pronounce it).
The great things about taxonomy with real names is the fun you can have with their coinage, as shown at this marvellous website.
Hosted by Flickr
Hell hath no fury like a thwarted taxonomy pedant. I used to look after agricultural journal, and nothing could make the editorial board members spit more than an author who dared to report a Latin name without the parenthetical suffix of the person’s surname who had bestowed the name.
And quite right too. It’s been a 20-year battle for me, here, to get anyone at all to take taxonomy seriously. Even now we have papers that get as far as publication without anyone remarking that any organism — any organism — should be referred to by its formal name. Molecular biologists are the worst. Happily, in these days of genome sequencing, even the brains of the molecule-obsessed have begun to stir sluggishly towards the realization that when one is acquiring data, it’s usually a good idea to know where it’s from before getting all enamoured of machines that go ping. AAAAARGHHHHH!
Wait Henry — are you saying that these proteins and whatnot come from different animals?
That changes everything.
(Would someone explain to me what an ‘animal’ actually is, please? Ta)
Richard – see photo above. It’s the thing under a pancake.
That doesn’t help, Brian — no scale bar.
In fairness, some of them know thale cress down to its genus.
Richard – see photo above. It’s the thing under a pancake.
I thought that the rabbit was suffering from some unpleasant helminthological infection.
Not all molecular biologists are as insensitive to these issues as you think, Henry.
Not all molecular biologists are as insensitive to these issues as you think, Henry.
Well, they are getting better, Jenny, because they have to.
Back in the day when all the molecular biology we knew came from a very small selection of model organisms, you’d mention ‘biodiversity’ to a molecular biologist and they’d give you that same vacant look you get from inner-city schoolchildren who’ve been told that vegetables grow in the ground and not in plastic bags in Tesco.
Then we’d have cases of three papers coming in at once, all working on the same protein, but each group had their own name for it, and would refuse to agree on a standard name. Apparently lab amour-propre was more important than understanding (an attitude I find quite reprehensible, actually).
Then people, usually of an evo-devo frame of mind, would start trying to branch out, workung on non-model organisms concerning which even the basic biology and husbandry was largely unknown, and who’d struggle to get simple expression patterns in scarce and precious embryos… and referees would get very sniffy and say things like ‘why don’t you do it in Drosophila instead?’
Now that molecular biology has caught up with
realold-fashioned biology, people look at all sorts of organisms all the time, so that, at long last, people who look at molecules are at last coming round to the idea that biology concerns a dazzling variety of endless forms most wonderful etc etc.I am not wholly innocent in this entire affair…
Well there you go. The problem isn’t the “genomics community”, it’s the biologists depositing the data :)
I’m with you on the use of NCBI IDs (GIs). Ultimately, the problem is one of indexing for easy retrieval. I don’t need a name that hints at function. I definitely don’t need a name that tells me nothing (bride of sevenless? Terribly amusing, bloody useless). If I know that what I’m looking for is GI:6226524, I can go and fetch it.
I really liked Euan’s idea of having version numbers on gene names, each linkable to a precise sequence, such that no ambiguity at all remains. There must be people working on things like this.
I was thinking that most of these efforts are probably going into the human genome, though. I wonder how thorough people will be with other organisms, especially those that are not major model organisms?
IUPAC, the draconian committee that keeps the chemists firmly in line
Your post put me in mind of IUPAC too, as a chemist manque (or perhaps that should be a chemist _oublie_).
But although everyone knows that chemists have nomenclature sorted … it is still a bit chaotic. Because IUPAC names didn’t make for well-organised indexes, Chemical Abstracts (CA) produced their own naming system, hence if you wanted to search for a substance you had to figure out the CA name rather than the IUPAC name. This is less of an issue these days as you can just do a structure search instead.
And of course chemists can be resistant to abandoning non-systematic names – who uses “methylbenzene” rather than “toluene”, for instance?
When I first started running literature searches for molecular biologists, back in 1989, I often despaired of the mess of gene and protein names (don’t get me started on problems searching for greek letters and sub/superscripts!). Perhaps it’ll be sorted out in another 20 years’ time.
Someone else has pointed out to me that chemicals are easy compared to genes: they don’t exist as a swarm of polymorphisms, so the set is finite. In a way it is reassuring that even with that simpler set, they are having problems.
This lit search thing must surely be the subject of heavy scrutiny, but I haven’t found much on where we are with this problem. I would have thought that PubMed at least would be interested in improving the situation – I wonder what they are doing.
….we have papers that get as far as publication without anyone remarking that any organism—any organism—should be referred to by its formal name…
Yes, Henry, but the trusty subs on the 4th floor or wherever they are sequestered are exercising constant vigilance.
This conversation has many, many echoes of the lot of the "person on the journal who cares about this sort of thing not just taxonomy but everything. What can I say? I think I’ll just go and collect my daughter from her school theatre trip, the time has finally arrived.
I forgot to close my inverted commas. Tragedy.
Constant Vigilance. And Total Concentration.
I can’t recall where I read this, but it was an old retraction, because the authors used the wrong expansion, of two possible, for their gene. Put the fear of God into me! I cling desperately to the CD-system of nomenclature in immunology but…
Neal: I don’t need a name that hints at function. I definitely don’t need a name that tells me nothing (bride of sevenless? Terribly amusing, bloody useless). If I know that what I’m looking for is GI:6226524, I can go and fetch it.
I guess, for me, it would be important to have a short, memorable name/symbol for the purposes of discussion and communication. When you are working with hundreds at one time, like me, it’s really quite useful to be able to discuss the dataset in a way that calls up the identity of the gene without having to look something up. Some of my fly genes, for example, don’t have names at all, but a string of five to eight numerals preceded by the letters CG. I’ve been working with some of these for a year and still cannot bloody remember what they are called.
No, I want to be selfish and have it both ways.
Maxine: I forgot to close my inverted commas. Tragedy.
Yes, but I had a lot of fun trying to guess where you meant to do it!
Niranjana, don’t get me started about the CD system. Again, I find it impossible to remember any of the pathways when all the names are so similar.
This is only one small aspect of these hugely important issues you touch on, Jennifer and everyone, but to respond to one suggestion about journals enforcing nomenclature consistency for human readers.
In some ways this is more practical for specialist journals, eg for a particular entity a genetics journal (or maybe a Drosophila genetics journal, in fact) can enforce the use of bride of sevenless (etc), whereas a bioinformatics journal can enforce the use of the set of letters and numbers that defines it. You can see where I am going: the more interdisciplinary the journal, the more difficult it gets to “enforce” one nomenclature for one entity (even without all the subtype, variant, polymorphism types of question).
So probably the answer is, as Jennifer indicates, some datamining solution which involves “behind the scenes” linking into databases, rather than the actual words on the page (printed or web) being the same every time that entity is used within that publication.
Of course, it is difficult to “enforce” even the most general nomenclatures, look at the sulphur/sulfur issue which was raging long before I joined Nature in the 1980s, and before the Internet was invented. Whatever nomenclature committees might decide, some scientists and some journals are not going to want to give up their rules of spelling/grammar, or house style, just because some collection of people (nomenclature committee) somewhere says so – they may do eventually, but it all takes time (cue in estrogen/oestrogen and many, many similar examples).
The text mining approach is the way I think – but in practical terms some way off yet. At the very basic end of it, most journals have print-based production workflows, with material post-processed for the web. As much of this material we are talking about is what is technically known as “special character” ;-), ie greeks, italics, superscripts, thinness of space between characters, and so on, many automatic coding systems do not work, or need constant vigilance to make them continue to work bug-free (not displaying gobbledygook).
We’ve hit this type of problem a lot in creating automatic editing tools for mark-ups of entities for the web that will not crash when applied to our journal editing and production workflow (document structuring, xml output for typesetter, etc). There are a lot of technical systems that interact and they sure aren’t all “interoperable”.
Maxine
All of my data is currently stored in a bespoke database, and some of the fields are constantly ‘looked up’. So for example, all the gene symbols for my genes aren’t typed in statically, but are actively pulled down from a genomics site (NCBI in this case). That means that what I see on my screen when I look up my data is responding to changes in the community’s nomenclature. The unique ID stays the same, but it used as a key to pull down all the current information about it.
In my dream, online journal articles would be encoded with the same keys. Gene names would be actively looked up and would change with the times. I know this is really difficult now, but one day I suppose journal articles will be a lot more dynamic. (None of the journals I’ve ever worked for will actually go into the xml of the post-publication online version and allow changes to be made in the event of errors, which I found shocking when I first found out about it. No, the scientific ‘record’ is still carved in stone, and the authors have to publish an errata. To me this seemed like madness – if you had an editable online version, why couldn’t it be changed I am sure one day these sorts of things will happen, once people stop thinking of articles as statics things in ‘print’.)
Wow. I want to see that system, Jenny. Sounds just like the sort of thing I need. I took my laptop to the poster sessions and looked up people’s favourite genes in my own database when we got talking. Linking directly in to deep functional information would be… awesome.
The thought struck me that I have a lot of control data that I should share, and maybe I should look into this, too. ponder. Blogpotfodder, I think.
I"ll definitely look forward to reading that post.
Yes, Jenny, (Jennifer?! I never know which to call you), that “behind the scenes” ability would be wonderful. The Semantic Web. Did you see this article in Molec Systems Bio, by the way?
PS, your comments about text in journal or archive articles (or anywhere) being dynamic — absolutely. The semantic web (or whatever one calls it – “the future” anyway) needs to be able to cope with evolution of and errors in nomenclature between the various places in which it is held or referred to.
Hum. A move away from static literature. Hypotheses refined on the fly. We need, of course, good tracking. But that is an interesting concept. It ties in, I think, with what Sebastian was trying to say.
Talking of IDs, how about unique alphanumeric IDs for authors? Some people change names, some people have the same names as others. ’Twould make things a whole lot more straightforward.
Richard – I want to be Number 6.
I heard someone from physics publishing a few years ago talking about living reviews, which can be updated as time goes on. Version control strikes me as a practical problem, especially for citation.
Hmm. With Firefox (sorry, Maxine), someone might be able to write a greasemonkey script that would automatically change the names of genes or proteins to what you are familiar with. Automatic search and replace isn’t perfect of course, but most names seem pretty unlikely to come up in normal text.
Well I’m the new number 2, so that works for me.
Yes, the alpha
malenumeric identifier for authors gets raised every so often. I am sure we have discussed it before on Nature Network because that is how I have ended up with this ClaimID “thing” which I have to log into every time I leave a comment on a blog somewhere. I wish I could remember who recommended ClaimID so I can ask them about how to get it to remember me!There is a letter in Nature Correspondence this or last week making the point about author IDs, but it is one of those perennial topics. Access controls are a tough challenge when interoperability between systems (over the whole internet as well as within organisations with different registration systems for different types of transaction) is needed.
Maxine, please call me Jenny. Can I call you ‘Maine’?
Citation and version numbers…yes, I see the problem there. But if everyone can site a version number that is archived as things change, this is covered, no? Much in the same way as people are asked by journals, when citing web pages, to record the date that they accessed that site.
Thanks, Jenny (it was the slight inconsistency in nomenclature and version control between your NN name and the name people in the comment thread call you that made me hesitate).
Yes, call me Maine, by all means! My typing fingers always do that when I write my own name, then I have to retrospectively add the x.
As for versioning of authors, pages, etc — I am no expert on the nitty-gritty. As you say, there are technical solutions in principle, but we need to achieve standards, annotation, etc. A doi gives an article a unique indentifier (hence the post-pub corrections you refer to above, etc). Web pages are less reliable, and if you’re a journal you try not to publish references to things that might disappear. But as you rightly say, I am sure it is possible technically to do these things, but I am also sure there are challenges in the implementation.
It strikes me that doi’s could be appended with version numbers quite easily, if everything was automated. Say your authors publish a paper with doi XXXX. Six months later there is a nomenclatural change, which is picked up automatically by the code that generates the online html version, and this code simultaneously changes the name in the text and modifies the doi to XXXX.1 (or whatever). Errata would have to be handled manually, but it still wouldn’t be too difficult for an editor to correct (say) a key misleading mistake in a figure legend and then upgrade the doi to XXXX.2, and so on.
I think a model similar to the one used for software could be applied. Each version has an x.y.z,for example R is now 2.7.1. The first number is the major release: a zero means it isn’t stable yet. A shift from 1 to 2 would mean that there have been major structural changes – this would be like re-writing a paper. The second number is for minor changes – a couple of functions added, or changed in the way they work. I guess this would be like re-writing small sections, or adding a paragraph to acknowledge that Spigot (1973) showed almost the same thing. The third number is for minor changes, bug fixes etc. Obviously this would be for typos and general tidying up (including changing gene names).
I think the problems are practical – firstly in setting up the administration, to track the changes and archive old versions so that they are readily available. I guess this just needs effort. The bigger problem might be in cross-citing different versions. I can see plenty of room for confusion there. I guess we would deal with it somehow.
Jumping in late here…
@Jenny: I hear your plaints, but thought everyone had already registered that HGNC was the ultimate reference – and they tell you as many of the “once known as” as they can get their hands on. So a simple search usually does retrieve what you need by way of synonyms. But I suppose if you’re not working with humans then there is no reason to think of HGNC in particular.
On the other hand, I am quite a fan of the public BioGRID and am regularly frustrated with their inability to keep up in the same way that Ingenuity does (which I see you tagged, but it’s really painfully expensive for a poor European lab, even with discounts). So money does buy you love. I do my best to annotate back to the community but, like you, I wish there was a way to be sure I caught all the synonyms. I usually settle for “best known” and cross-check among different softwares and platforms. There is no one-stop shopping.
@Henry: I work often with gene expression patterns in human embryos, which are indeed scarce and precious. I regularly get that very expression you cited from referees, but with respect to Mus rather than Drosophila. Sigh.
And to support the idea of citing article version numbers, one already must cite which NCBI genome build one is using, since those builds change regularly and dramatically.
“So a simple search usually does retrieve what you need by way of synonyms.”
Each gene has an average of 10-20 synonyms from what I can see. I am dealing with 600 genes. Sorry, but I don’t have ten years to sit in front of PubMed searching for all of them.
So…this very comment thread is being used as an example of everything that’s “wrong” with Nature Network, in a comment thread about this post on FriendFeed which ironically develops way more in a tiresome mess than this does. And also ironically, this very comment by me is one of the few off-topic ones in this thread so I’m contributing to the “problem”.
(I feel kind of like a FriendFeed-traitor by linking it here, but I also feel bad when people say they don’t want to use Nature Network when I’m trying so hard to get people over here.)
Personally, if I’d have wanted to make a statement about pointless chatter on NN, I would have used this post. ;)
HEY, that doesn’t work without the link.
Retake (and feel free to delete that previous comment if possible)
Personally, if I’d have wanted to make a statement about pointless chatter on NN, I would have used this post ;)
Wow, Eva, I didn’t realize there were people out there like Neil trashing my blog! Thanks for the tip-off. (I’m not upset, just amused.)
Personally, I have to disagree with him and the others. First off, this comment thread raises several interesting solutions, for example the stuff about version numbers and doi’s, and has made me think. Second of all, a little humor and levity in life is no bad thing. If those FriendFeed people were chatting about a knotty science problem down the pub, would they get angry if someone digressed to tell a joke or make a witty observation? Probably not. I guess I never forget the “social” in social networking, and I don’t feel one has to be Serious and Earnest all the time.
Let me be clear, Eva: I don’t mind people going off-topic in my salon. So please never feel bad for doing so! I really appreciate your contributions.
Fascisms is for…well, fascists. :-)
I suspect there’s more than a little bit of jealousy involved.
Either that or they’ve exceeded their levity quota for this year.
Look, I’ve seen blogs with ‘serious’ comment threads, and frankly, they can stick it.
I think there is a lot to be said for the light-hearted approach, especially with science. (This is, for example, the essence of our approach at LabLit). Humor can attract in people who might otherwise stay away.
It never occurred to me that it could repel people, but then, I’ve got a sense of humor.
er …. Mornington Crescent?
Nah, that’s not funny at all.
Apologies. I shall now go into a dark corner and commit origami.
Just don’t crane yourself.
That friendfeed page really irritated me. The levity is one of the good things about it. Heavens, if one were to criticize NN for anything, that would be way down the list.
Eva – I’m suspect my bunny contributed to the FriendFeed moan.
I do find that attitude very sad – these have to be the kind of people who give science a bad name, and for whom “get a life” isn’t bad advice.
What they seem to miss, apart from the importance of humour (no doubt to come up in the creativity/blogs discussion at the Science Blogging 2008 thingy), is that a network like NN has people from a range of backgrounds and disciplines, who will contribute differently depending on the topic.
Sad indeed.
Thanks, Henry – that saved me from a small explosion. The roll-on-the-back-to-have-the-tummy-tickled manoeuvre has to be one of the most powerful in the Golden Retriever’s armoury.
“What they seem to miss (…) is that a network like NN has people from a range of backgrounds and disciplines”
That was the strangest part to me. One comment thread is now representing all of Nature Network? I usually get on-topic comments in my blog, and I’ve had very useful on-topic conversations on some of the forums.
I think, for better or worse, the early adapters of NN have tended to be fans of wit, whimsy and intellectually amusing banter (you know who you are). My own blogs may attract this even more, as there is usually a humorous edge to my posts. Later adapters copied the spirit of the initial pioneers – for which I am happy. I hope the atmosphere stays this friendly, entertaining, helpful and remarkably whinge-free even when it outgrows the regular crowd.
I think you mean adopters. Adapters are things you attach to plugs, or, possibly, molecules in the VDJ recombination system (don’t shoot me I’m the
pianistpalaeontologist). Oh, f**k it.The roll-on-the-back-to-have-the-tummy-tickled manoeuvre has to be one of the most powerful in the Golden Retriever’s armoury.
For sure but of course Heidi adopted/adapted this from her Master ;-)
Perish the thought.
A bit late to this one, but having read Corie’s post, I get what is going on. I have been reading a lot of comment on that FF group over the past few days about Declan’s news story in Nature, where disagreement with what he writes is translated into personal comments more suited to, er…..can’t think but there are some photos above.
Anyway, I put a comment in the FF thread, which is probably both daft and rash. (I experienced a bit of the same group’s behaviour on the online commenting thread to Declan’s news story.)
I very much enjoy your blog posts and comment threads, Jenny, and from their length, clearly so do other NN users (who do not stoop to Cleggian experimental tactics to make ’em long!)
I think your comments above to the FF page are spot-on, Jenny. Eva, I liked the comments you made there and here.
Thanks for the support, Maxine et al. Someone pointed out that it’s all good publicity.
Henry: adapters. Yes, well, I’m a bit tired, been slaving over a hot Bunsen burner all day, up to my elbows in cancer cells and inscrutable nomenclature. It’s so nice making an error here – you can rest assured that your
Naziconcerned friends will gently correct…I thought Declan’s story was good, for the record, except as seems to be Nature’s unspoken policy, BioMed Central is never, ever credited as being the first open access publisher, years before PLoS.
Oh I dunno. I like the thought of being an early adaptor.
I also like the way you seamlessly worked in the gratuitous link to LabLit, which by the way now has a Facebook page.
Gratuitous?
How dare you, sir.
For sure but of course Heidi adopted/adapted this from her Master
Come down here and say that. You’d look good arguing for open access with no f***ing teeth (Oh, by the way, nothing personal. How am I doing for nastiness? Sufficient recreational outrage?)
I think you need a bit more of an edge, Henry. Also, angry people often write carelessly, so throw in some typos for verisimilitude.
Dang it. Three days of intensive exposure to Pharyngula comments threads and I still come over the English Milord. [Note to self: quit mainlining the Marmite and stop listening to The Archers
So there I was, creating a cute fluffy image of Dr Gee playing with Heidi and I get the red hot skewer treatment in return !! – Grunt
You is too blunt Ghee and I agree with Jenny in that you need more hedge (preferably a v. large one).
Yes, if we all want to survive in this cutthroat nasty online world, we need to learn how to be a lot less courteous and friendly with one another. No more Dr Nice Guy.
Your hedge has too much…privet. And not enough oak. So there.
Dr Rohn, your roses need dead-heading. Shocking, they are.
Ptth.
[Yes, I could get used to this.]
Oh come on woman. Show some spunk. Let’s have a rib-rattling retort, with rolléd r’s.
I suggest that we be nice and polite on these fora, perhaps devolving our nastier urges onto surrogates.
Fucking fuck off, you fucking republican creationist scum-bag!
More tea, vicar?
There is milky, sugary coffee now firmly intercalated in my keyboard, Henry, and it is all your fault.
All your fault for taking sugar with your coffee. Rots the teeth, you know.
And milk.
Sugar rots milk?
Interesting thesis.
It’s the new paper-scissors-rock thing you know.
sugar rots milk
milk spoils coffee
coffee dissolves sugar
Must be a Brit thing.