Nascent tweet sequences visualise peer review at LOLcat resolution

There’s never a dull moment.

Earlier today, I read a paper from Nature titled “Nascent transcript sequencing visualizes transcription at nucleotide resolution*”. The paper describes a very cool new technique that allows you to see gene transcript sequences as they are being made. The authors demonstrate that this method can be used to sequence unstable, short-lived pre-modification mRNAs; quantify sense and antisense transcript abundance; identify proteins that regulate promoter directionality; and map transcription pause sites.

Cool stuff, right?!

(If you’re not in this field: trust me on this. It’s megasupercool).

So, this article being in the same issue of Nature as a feature on rapid online post-publication review (“Peer review: Trial by Twitter“), I obviously had to tweet about it. And that’s when the fun began:

Twitter is fun

In no time at all, Bob maded me a LOLcat, and then he eated tweeted it:

OHAI! I can haz sequences of gene transcripts  as they iz being maded!  Can seez what they iz looks like before nomming

Genius! Ribosome Polymerase Kitteh iz teh LOLz!

The Nature feature on online peer review says:

“Unstructured, unruly and often anonymous, online commenting can be exasperating for biologists used to more conventional means of discussion”.

I can’t possibly think why.

……………………………………….

*Full citation: Churchman LS, Weissman JS. Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature 2010: 469:368-373.

I’d also just like to say that Stirling Churchman is an awesome name.

Posted in communication, furry friends, original research, publishing, science, silliness, technology | 56 Comments

Hockey pool, week 15

Well, seeing as I completely forgot to organise who was doing which update, I’ll host this time – and try to do better next week!

Lavaland (at the very top) and Thomas (at the very bottom) tied for the week’s best performance, with 31 points each. Ricardipus was next, opening up a mighty one point lead over Bob. But can either of them catch Lavaland?!

Chall beat Gerty’s weekly score by one point, increasing her lead over 5th place Gerty to… two points!

ScientistMother brought up the rear in the weekly tallies, allowing me to make up some of the ground between us. But I have at least one eye on my rear-view mirror, with Thomas making a run for 7th place!

I don’t seem to be able to change my picks right now – there’s some kind of glitch with the system – so hopefully we’re all in the same boat! Could be an interesting week…

Posted in hockey pool | 11 Comments

The scope of horoscope horror

My friendly local morning news team are discussing horoscopes today. This is, unfortunately, nothing new; I had to change the channel on New Year’s Day because their guest astrologer was doing my head in with her “Scorpios will come into some money in April” crap.

Today’s angle was the “news” that some astrologers want to change the birth dates that correspond to the different signs of the zodiac (H/T Noah Gray, on Facebook, for the link). Don’t worry, though – other astrologers don’t agree, so if your star sign is critical to your sense of identity (or if you have your star sign tattooed on your arse), you don’t have to change if you don’t want to.

(Even if the dates change, my sign won’t – I’d still be an Aquarius, by the skin of my teeth, under the new rules. You can imagine how relieved I am to learn that this major schism doesn’t affect me at all).

Now, I suppose I can understand so-called news programmes covering astrology. It’s still incredibly popular, after all, even if it has been pretty comprehensively debunked. And it’s a light, fluffy item they can cover with zero research, opting instead to compare old and potential new star signs with the meteorologist and traffic reporter. Whatever – I have the choice to switch off the TV and write a blog post instead, with some nice sensible podcasts playing in the background.

What bugs me is how ubiquitous astrology still is in daily life. People bring it up all the time, and I wish it was socially acceptable to mock them loudly. But unfortunately, the subject mostly arises in situations where I have to grit my teeth and nod politely, or – worse – join in. For example:

  • I once walked into my lovely mother-in-law’s house to see that she’d cut the New Year horoscope section out of the local paper, annotated each horoscope with the names of all family members (including me) who fall under that sign, and intended to keep the damn thing stuck up on the fridge (obscuring some awesome new photos of her grandkids) all year. But what can you say?!
  • My ex-boyfriend used to blame every single moment of indecision – from whether to move to a new lab to choosing between pizza and curry for dinner – on “maybe it’s because I’m a Gemini*”. (OK, I may have mocked him occasionally, saying “you’re a scientist, FFS!”, but he’d actually get upset about it, so I mostly stopped. Mostly).
  • An ex-flatmate once told me that things weren’t going to work out with the guy she’d been on a few dates with because “he’s a nice guy and all, but he’s a Capricorn”. OK then.
  • I remember some blog buddies who use Blogger being outraged a couple of years ago because adding your birth date to your profile meant automatically displaying your star sign, too – there was no way to separate the two.
  • In a project meeting with a mix of clinical and research colleagues, all senior to me, one person wished another a happy birthday. Another member of the team piped up with “ooh, it’s your birthday today?! That makes you, um, a Virgo, right?!” She then went round the table asking everyone else to say what sign they were.

This last one bothered me more than all the others put together. No-one else seemed to bat an eyelid, but I was astonished – I kept thinking “but we’re scientists! We’re here to discuss a cutting edge genomics-based translational research project!” I have the greatest of respect for everyone who was in the room that day – they’re lovely people and dedicated professionals – but c’mon. REALLY?! C’mon. I have to discuss my star sign politely and with no mocking, AT WORK?!

That’s asking a lot.

There has been one recent exception to my usual polite responses to horoscope conversations. I was at my friends’ daughter’s first birthday party, along with lot of other mutual friends and acquaintances. I may have had an afternoon beer or two, never a good idea for this lightweight. A woman I know well enough to know that this kind of topic is fairly typical for her was saying how nice it was that the birthday girl got to be a Cancer “because that’s a nice sign”. I nodded and smiled, but then she asked me what sign I am.

“Um, Aquarius”, I replied.

REALLY??!! NO WAY!!“, she replied. “Are you sure?”

(I was)

“You must be on the border with another sign, though?”

“Nope. I’m right in the middle of Aquarius, with an Aquarius moon and rising Aquarius”, I said.

(I only know this because my auntie bought my sister and me books about our star signs for our birthdays one year when we were teenagers).

NO WAY!!! I NEVER would have thought you were an Aquarius!!!!” she squealed. “Never in a million years!”

My reply?

“Well, what does that tell ya about the value of astrology?”

I don’t think she got it.

Maybe it’s because she’s from the sign of the bull.

—————–

*I just checked, and under the proposed new dates he’d actually be a Taurus. HAHAHAHAHA! Shall I email him and tell him?

(Rhetorical question. Things did not end well, to say the least (let’s just say that he cheated on me and as a result we both had to take an HIV test – negative, thank fuck) and we’ve had zero contact for ten years; I’m more than happy to keep it that way, whatever star sign he is!)

Posted in career, current affairs, drunkenness, family, idiocy, personal, pseudoscience, rants, television, the media | 43 Comments

It Gets Better

(ETA: DAMNIT! I still can’t figure out how to embed videos. I’ll try to fix this later, but for now I’ll just put the links in)

(E again TA: Richard fixed the embedding! Yay! Thanks again, Richard!)

(3rd edit: adding the above edit borked the embedding again. Sorry. I’ll try to fix this at some point over the next day or two.)

I’ve mentioned before how much I freakin’ love Dan Savage, and especially his “It Gets Better” campaign to bring hope to GLBT teens being bullied in high school. This week’s episode of the Savage Love podcast highlighted a related song by Rebecca Drysdale; as soon as the episode was over I went to YouTube to find the video, which I wanted to share with you!


(NSFW)

Having been bullied all through high school myself for being a swot and a teacher’s pet, I especially appreciate the shout-out at the end to the straight kids who also get victimised. I can’t imagine how much worse I would have had it if I’d been a lesbian swot and teacher’s pet, though.

While we’re on the topic, here’s the “It Gets Better Canada” video:

I think I love Rick Mercer even more than I love Dan Savage! In fact, here’s more on the same theme from Rick, just because he’s lovely:

Posted in Canada, education, embarrassing fan girl, music, personal, videos | 17 Comments

Hockey pool, week 14

Well, after the exciting changes in the rankings in weeks 12 and 13, this is a wee bit of a dull installment:

Yes, there was only one change in position, by GertyZ; her table-topping weekly score of 34 points was enough to propel her from 6th to 5th, and almost enough to catch Chall in 4th. Bob also had a good week, with 31 points, and is now in joint 2nd place with Ricardipus.

Lavaland and ScientistMother were this week’s laggards, with 21 points each. Lavaland still managed to hold onto a 10 point lead at the top, though, and ScientistMother looks to be in no imminent danger from either myself or Thomas.

Personally, I find the graph above to be slightly depressing viewing, and I prefer to look at this table instead:

WE! ARE! TOP OF THE LEAGUE! SAY WE ARE TOP OF THE LEAGUE!

(It’s my ambition to introduce proper football chants to the NHL, or at least to the Canucks, but no-one will ever chant along with me at live games, and my voice isn’t loud enough by itself).

Would anyone like to volunteer to host the next update(s)?!

Posted in hockey pool, sport | 15 Comments

Fear o’moans

I’m sure you’ve all heard by now of the publication in Science this week of a study suggesting that pheromones in women’s tears reduce testosterone levels and sexual arousal in men (summarised by Ed Yong here). This is definitely not my field, so I won’t attempt to add to the blogosphere’s ongoing analysis of the paper. However, I would like to share with you a (vaguely) related episode from high school…

I was with my A Level chemistry class (three male and two female students, and a female teacher), so we must have been somewhere between 16 and 18 years old. We were all standing on the benches of the science lab, not as an homage to Dead Poets Society, but because the room was freezing; our teacher had just returned from the staff room with a space heater, and was taking advantage of this opportunity to demonstrate how convection heating works. It was noticeably less frigid up there near the ceiling, and as we warmed up we were discussing a documentary about pheromones in moths that a few of us had seen on the BBC the night before.

Now, while my female friend and I were doing biology as well as chemistry A levels, all of our male counterparts were doing physics instead. (Not one student in my year did all three). One of these male students had never heard of pheromones before, and was asking lots of questions. Our teacher had seen the documentary too, and was listening in, but was letting my female friend and me take the lead in answering all questions.

Our male friend seemed to be gradually leading up to something, and finally blurted out, “do humans have these pheromones, too?”

“I think so”, I replied. “They didn’t really get past moths on the programme last night though”.

“Oh, yes, humans have pheromones”, added our teacher. “We’re probably influenced much more by smell than we’re consciously aware of”.

“So…”, continued the male student, “humans can give off scents that let other people know that they’re attracted to them?”

He looked increasingly worried at this point.

“Yes”, replied our teacher.

“OH!”

He was definitely getting quite agitated by now.

“From, like, how far away?

He blushed bright red.

It took him a while to live that one down…

Posted in education, original research, science, silliness, TMI | 14 Comments

Instant karma

An acquaintance at a funding agency emailed me today, asking if I had contact information for a researcher I’d never heard of. I didn’t, obviously, so I Googled the person’s name from the search box on my browser toolbar. The first page of hits on the main Google page were all for an actress (who I’d also never heard of) who has the same name as the researcher in question.

A young and attractive actress.

Undeterred, I initiated my standard response of typing in the researcher’s main field after the name that was still in the search box.

Unfortunately, the researcher’s main field is breast cancer.

The Google Instant hits for “YoungAttractiveActressFirstname Secondname” breast were, um, interesting.

Just another occupational hazard.

(As it turns out, my acquaintance was actually thinking of a researcher with the same surname and first initial as the actress in question, but with a different first name. I did have her contact information, and her Google Instant hits are much more conventional).

Posted in career, science, silliness, technology, TMI | 8 Comments

And the winner is…

Thanks to everyone who voted in the Second Annual VWXYNot? Readers’ Choice Comment of the Year Award!

It was a close race between the top three contenders, but luckily for me we have a clear winner, and I don’t have to cast a deciding vote!

RPS77 wins!!!

The full winning comment was “Just think – until the development of the internet, bathroom graffiti was almost the only way for strangers who never saw each other to exchange random insults.”

Congratulations, RPS77! Very nice work. Email me at vwxynot [at] gmail and let me know which email address to send your Amazon gift certificate to!

(Henry and Chall, you too – I still haven’t sent you your prizes as I don’t know which email addresses you use on Amazon!)

Thanks again to everyone for your comments and friendship in 2010 – and I’m looking forward to an excellent bloggy 2011!

Posted in blog buddies, meta | 11 Comments

Do The Art, Man!

I’m a big fan of the visual abstracts that many journals have introduced recently (even if they do make scrolling through TOCs in Google Reader like wading through treacle at times); I’m a very visual person, and I find it much easier to look at diagrams of signalling cascades than to read about Protein Blah activating Protein Meh, which activates Protein Whatever, which phosphorylates Protein Who Cares.

I haven’t seen any summary cartoons that include sharks and crabs yet, but I did enjoy this one, from today’s Current Biology:

Cowabunga, dude!

Awesome.

HAPPY NEW YEAR to all my lovely readers! I hope you have an excellent night, and a fantastic 2011. 2010 will be hard to top for me, but I’m very optimistic about Good Times ahead!

Posted in art, original research, publishing, science, silliness | 24 Comments

Book ’em!

Well, the bookcase Mr E Man got me for Christmas may not have been a surprise, but it sure is awesome!

Before:

Try finding a specific volume in this mess!

Books behind books on top of maps...

+

Beautiful virgin territory

During:

Google books

(She also hopped into the dresser while I was emptying it, but I didn’t manage to get a photo. She’s very helpful).

After:

Books! Beautiful orderly books!

+

Returned to its original purpose

SO. MUCH. BETTER!

While I was moving and organising my books, I kept thinking “Oh, right! I meant to review this one on my blog!” My book reviews tag has been sadly underused this year, and I don’t really remember the details of all of the books I’ve read since I posted my last review, but here’s my attempt at catching up!

Midnight’s Children by Salman Rushdie

This was a really, really challenging book. I don’t remember finding any novel quite so difficult to read since I started tackling “proper literature” in my early teens. It took me several attempts to get past the initial few chapters, but while we were on vacation in Cuba I finally managed to push through to the stage where I just had to keep reading to find out what happened .

I’m really, really glad I persevered, because the book is a gem. I love Rushdie’s use of language (and had to be very vigilant about not copying some aspects of his trademark style into everything I wrote while I was reading this book!), and it’s a very rich story; it starts with the main character’s grandfather as a child, which gives you a sense of the historic span of the book, and it’s incredibly densely packed with characters and events. This is the main reason I found it so difficult to get into, and the main reason it was so satisfying.

My one regret with this book is that without a very strong grasp of the history of India, Pakistan and Bangladesh, some of the impact of the story no doubt went right over my head. The lives of the main character and the rest of the Midnight’s Children (those born at the moment India became independent) mirror the story of India, and while I know enough to recognise a few of the analogies, my level of education in the history of the region definitely let me down. But even if you’re in the same boat as me in that regard, I’d still recommend this book if you feel like a challenge!

The Satanic Verses is in my pile of unread books (stacked horizontally on the fourth shelf of my new bookcase!) I hope it’s a leeetle less difficult to get into…

An Equal Music by Vikram Seth

This is a love story about a professional violinist in London who rediscovers a former lover. Classical music features prominently, to the extent that it’s essentially a character in its own right; the events within the novel are intertwined with descriptions of several works, from the professionals’ point of view. It’s very well done; I wasn’t familiar with all of the pieces, but the book is so well written that this really doesn’t matter. Familiarity with any music (and especially playing it within an ensemble) is enough.

Overall, I quite liked this book, but I didn’t love it. It didn’t grab me on an emotional level. Part of the reason may be that having been cheated on myself by a long-term partner many years ago, I find it hard to be sympathetic to a relationship-wrecking main character, so your mileage may vary!

I won’t be keeping this book, so give me a shout if you’d like it! (Eva…?!) I’d be happy to mail it anywhere – surface, of course – maybe in return for a used book of your own…? 🙂

Birds Without Wings by Louis de Bernieres

I bought this book from GrrlScientist as part of her massive Transatlantic moving sale last year, and I loved it!

The story is set in Turkey before, during and after WWI, and begins with an introduction to the various inhabitants and customs of a mixed Christian and Muslim town. This part of the book is utterly charming – and riveting, despite the introduction of at least one new character per short chapter! The stories from the town are interspersed with snippets from the life of Mustafa Kemal and his rise through the ranks of the military; this, coupled with some knowledge of history and a familiarity with de Bernieres’ style, made me desperate to cling on to the tales of a happily integrated town and its inhabitants, knowing that things would go very, very wrong very soon…

…and, indeed, just as in Corelli’s Mandolin, when the war begins the descriptions of the battles, the living conditions in the trenches at Gallipoli, and the atrocities committed by both sides, were harrowing to read. No details are spared, no punches are pulled. It’s gruesome – but incredibly well written and engaging, even through the worst of the worst. My high school history lessons had covered some of these events, including the Gallipoli campaign and the rise of Kemal, which made it all the more interesting to me.

I’ve passed this book on to a Turkish friend of mine who grew up in the region described in the book. I showed her the book in the pub one night when I was about halfway through it, and it led to a fascinating discussion about many subjects, but especially about religion, history, and how they’re taught in English and Turkish high schools. I can’t wait to hear what she thinks of the book!

The Strain by Guillermo Del Toro and Chuck Hogan

Mr E Man and I unaccountably forgot to pack any books when we headed off on our five-day kayak trip in Desolation Sound this summer, and found ourselves in the terrible situation of having to buy books in Safeway while we were stocking up on food. This was the only book we found that looked even remotely readable, and to be honest we only bought it because of the author (yes, it’s the same guy who directed Pan’s Labyrinth).

I won the first turn at reading the book in a game of rummy, and formed a fairly negative opinion very quickly. I informed Mr E Man that it read like a screenplay rather than a novel, and that the writing was similar to Dan Brown’s.

However, this booked reeled us in SO QUICKLY! We ended up arguing constantly about whose turn it was to read it, and whether turns should be based on the number of pages or the number of minutes (I’m a faster reader than him, so of course I favoured the latter while he thought the former approach was fairer). It’s much better than anything Dan Brown’s ever written – extremely gripping and well-paced, even if the subject matter is a little hackneyed.

Yes, it’s a vampire book, but these aren’t your drippy, sparkly, teenage fantasy vampires – they’re grotesque, painfully diseased, and deformed – old-school, old-country vampires. It’s great stuff, and by the end I was totally hooked! I can’t wait for the next two books (yes, it’s a trilogy) and, most of all, the (surely inevitable) first movie!

Moving on to the less serious books on the list…

Sense and Sensibility and Sea Monsters by Jane Austen and Ben H. Winters

Everything I said about Pride and Prejudice and Zombies last year also applies to this book: it’s laugh-out-loud hilarious, tons of fun, and extremely silly indeed. At first I thought the side-story – the invasion and siege of England by a variety of grotesque marine dwelling nasties – had more of a narrative to it than did the plague of Dreadfuls in P&P&Z, but ultimately the story wasn’t developed and never resolved.

But really, who cares?!

Very highly recommended – just be careful about reading it in public, as involuntary and very undignified LOLs are a definite possibility.

The P&P&Z prequel is also in my pile of unread books!

I See Rude People: One Woman’s Battle to Beat Some Manners into Impolite Society by Amy Alkon

I read Alyssa’s review of this book and went straight to Amazon to order a copy for myself. The author is a self-styled member of the Rude Police who calls people on their rude behaviour in a very entertaining way that makes me wish I wasn’t quite so British all the time. She calls people back who’ve had very loud public phone calls that involved giving out their phone number and chides them for their rudeness; she tracks down anonymous trolls from the comments section of her website and calls them to invite them to repeat their insults in person. It’s all very amusing to those of us who also get worked up by other peoples’ lack of manners – but it also got rather repetitive towards the end.

This is another book that I don’t plan to keep, but that’s definitely worth reading; again, let me know if you’d like me to mail it to you! (Again, maybe you can mail me one of your unwanted books in return!)

I think that’s it…

I’ve also re-read a lot of old favourites this year, including the entire Hitchhiker “trilogy” and the two Dirk Gently books, plus all the much-loved John Wyndham books my parents brought over in May. But for some reason I just don’t feel inspired to post reviews for old favourites – sorry! You’ll just have to read them yourselves.

Mr E Man says I’m not allowed to buy any more books until I’ve read all the ones I already own. But I’m already making a list of books to buy next, and recommendations are always welcome!

Posted in blog buddies, book review, drunkenness, education, furry friends, photos | 22 Comments