Bar Graph

‘I just don’t see the point anymore….’

Where to go when ‘da data don’t fit’? When the p-values aren’t shaking out? When the theory isn’t stacking up? Where to drown your sorrows? Well….why not join the dots at ‘Bar Graph’ and wallow in the ‘pointless-ness’ of it all. Got some ‘axes’ to grind? Can’t see any ‘significance’ in your research? The friendly ‘barman’ (…or should I say bar-graph person?) is always there for you…well almost all of the time …maybe 95% of the time?

 

You can follow et Al. on twitter@lopsidedlablife

It’s Nice-2-Alt Splice – a music video

Well, I’ve only gone and made a music-video on ‘Alternative Spicing’, haven’t I. It had set out to be a bit of an homage to Scottish band Aberfeldy’s brilliant song/video ‘Tom Weir‘, with the lyrics modified to try to explain, in a fun and un-complicated way, a post-transcriptional gene expression mechanism called Alternative Splicing.  Anyway, hopefully I’ve achieved a little bit of the latter, but somehow along the way the indie-folk Aberfeldy vibe morphed into a kind of late 1980’s Simple Minds synth feel, finishing up with an Ibiza-rave themed finale.

I’d wanted to showcase some research that I do, and thought it’d be quite fun to try a song – so I gave GarageBand a go, and together with a few bits of guitar, and playing around with words and images on iMovie, came up with the final version – it’s posted, here, on our research group blog. I had originally tried adding some vocals but just adding text on the video was way better – I am, unfortunately, no Jim Kerr…

Anyway, I’m particularly proud of the lyric ‘It’s Nice to Alt Splice‘ – surely a contender for an Ivor Novello award, no? I found the whole exercise to be very useful – from learning the basics of GarageBand and iMovie – to also just trying to distill what I do down to the very basic and easily digested nuggets of information. As scientists, we are increasingly being encouraged to try to explain our work to anyone who might be in the slightest bit interested, from school kids to government policy makers. I think that this is very difficult for scientists – as they themselves are also often grappling with what they are doing. Even just to say the very banal – ‘It’s Nice-2-Alt Splice’ – is simple, fun and liberating – we can discuss the complicated bits another time, yeah?!

You can follow et Al. on Twitter @lopsidedlablife

Tubus tubulus

Figure(d) Tubus sp. from left to right; Tubus grandis, T. eppendorfis, T. minieppendorfis, T. pcr spp. flatlid and T. pcr spp. roundlid. Botton right; aggregates of T. pcr

 

Labs are usually ‘crawling’ with tubes – ranging from the larger, more common Tubus eppendorfis spp. microcentrifungus to the smaller Tubus pcr spp. flatlid and the closely related spp.roundlid (see Figure(d), above). The former has a remarkably varied diet and will sustain itself on many everyday lab solutions such as NaCl, buffers, BSA protein, and sometimes even DNA and RNA. The latter, however, survives in more specialised molecular ecological niches and relies on specific amounts of magnesium chloride, DNA polymerase enzyme and plasmid DNA. If caught and tamed T. pcr is more gregarious than T.eppendorfis – enjoying Master Mix cocktails, tube tickling sessions, and can be lost for hours on long hot cycling trips. On the other hand, T.eppendorfis likes nothing better than the rigour of a right good vortexing to mix up it’s lab ‘soup’.

Some Tubus sp. are on the endangered list with numbers of T. grandis (top left, Figure(d)) markedly declining – presumably as a result of extreme competition in the ‘consumables jungle’. Concerns about the future of Tubus sp., and the growing  awareness of their benefit to Science, has led international consortia – led by a group in Tübingen – to propose the whole plastic sequencing of Tubus (employing the new, next-gen ‘Plast-seq’ platform). Here, the omnipresent Tubus eppendorfis is mooted as the ‘reference’ Tubus ‘plast-ome’. Intense research has sought to identify the last common ancestor of Tubus sp. and recent indications point to the emergence of Tubus from around 1953 in the area around The Eagle pub in Cambridge, UK, although there also seems to have been several major duplication events around 1975 (known as the ‘Sanger-ian Epoch’), and a decade later in California (known as the ‘Mullis-oic Age’).

Fig(ed) An example of domesticated Tubus pcr corralled into a rack, ready to join a HighThroughput community

 

Tubus eppendorfis can usually be easily spotted roaming labs, not uncommonly in ‘packs’ of 500, but can also be found in smaller groups – typically on the Savannahs of exposed bench tops, and can be tamed or corralled into ‘racks’ (see Fig (ed), above).  Recent evolutionary adaptations has seen T. pcr develop the ability to aggregate in groups of 8 ‘strips’ (see also Figure(d)) thereby gathering as defined communities, known as HighThroughput communities. Politically this has led to some tensions within groups of the Tubus species, with the LowThroughput community complaining of marginalization from opportunities to advance the case for Science.

The future for Tubus sp.? Climate change…population explosion…er…flooding….mmm…Armageddon…..one thing is needed ….drum roll…….drum roll….More Research Needs To Be Carried Out !

You can follow et Al. on The Twitter @lopsidedlablife

‘It’s About Time’ – a science blog

Recently I’ve been busy getting our lab’s research blog up and running on WordPress. It’s called ‘It’s About Time‘ and is about our research into circadian clocks, alternative splicing, and how plants respond to temperature.

We’re also collaborating with artist Ally Wallace on a Art-Science project, the aim of which is to help scientists reflect on the skill of creativity with the spin-off being that it will help us tap into creativity in our own scientific work and also be better prepared to put across complex scientific ideas.

Hope you can drop by soon…..if you have the time

‘Used Tips’ – the collection

‘Used Tips‘ – a collection of throw-away nuggets of sci-thought. Sometimes whimsical. Sometimes ironic. Sometimes random. Hopefully always pleasing.

You can follow et Al. on Twitter @lopsidedlablife

 

Used Tips – ‘faith’

Used Tips – ‘bliss’

Used Tips – ‘confession’

Used Tips – ‘homologous’

Lets start 2015 with a Fizz-ics lesson….

Peter Higgs, a Physicist……

 

Peter Hics, a Fizz-icist

 

All The Best for 2015!!

et Al.

…and may all your Nucleosomes be bright!

Have Yourself a ‘Double Helix Christmas’….and may all your Nucleosomes be bright

All together now….

On the first day of Christmas my lab love gave to me:

• A knock-back from the E-di-tor

On the second day of Christmas my lab love gave to me:

• 2 peer reviews, and a knock-back from the E-di-tor

On the third day of Christmas my lab love gave to me:

• 3 standard errors, 2 peer reviews, and a knock-back from the E-di-tor

On the fourth day of Christmas my lab love gave to me:

• 4 re-submissions, 3 standard errors, 2 peer reviews, and a knock-back from the E-di-tor

On the fifth day of Christmas my lab love gave to me:

• 5 Hy-poth-e-ses, 4 re-submissions, 3 standard errors, 2 peer reviews, and a knock-back from the E-di-tor

On the sixth day of Christmas my lab love gave to me:

• 6 impact points, 5 Hy-poth-e-ses, 4 re-submissions, 3 standard errors, 2 peer reviews, and a knock-back from the E-di-tor

On the seventh day of Christmas my lab love gave to me:

• 7 tips-a-racking, 6 impact points, 5 Hy-poth-e-ses, 4 re-submissions, 3 standard errors, 2 peer reviews, and a knock-back from the E-di-tor

On the eighth day of Christmas my lab love gave to me:

• 8 channels pipetting, 7 tips-a-racking, 6 impact points, 5 Hy-poth-e-ses, 4 re-submissions, 3 standard errors, 2 peer reviews, and a knock-back from the E-di-tor

On the ninth day of Christmas my lab love gave to me:

• 9 reps-a-ringing, 8 channels pipetting, 7 tips-a-racking, 6 impact points, 5 Hy-poth-e-ses, 4 re-submissions, 3 standard errors, 2 peer reviews, and a knock-back from the E-di-tor

On the tenth day of Christmas my lab love gave to me:

• 10 degrees of freedom, 9 reps-a-ringing, 8 channels pipetting, 7 tips-a-racking, 6 impact points, 5 Hy-poth-e-ses, 4 re-submissions, 3 standard errors, 2 peer reviews, and a knock-back from the E-di-tor

On the eleventh day of Christmas my lab love gave to me:

• 11 mutant screens, 10 degrees of freedom, 9 reps-a-ringing, 8 channels pipetting, 7 tips-a-racking, 6 impact points, 5 Hy-poth-e-ses, 4 re-submissions, 3 standard errors, 2 peer reviews, and a knock-back from the E-di-tor

On the twelfth day of Christmas my lab love gave to me:

• 12 missing data, 11 mutant screens, 10 degrees of freedom, 9 reps-a-ringing, 8 channels pipetting, 7 tips-a-racking, 6 impact points, 5 Hy-poth-e-ses, 4 re-submissions, 3 standard errors, 2 peer reviews, and a knock-back from the E-di-tor

Merry Christmas everyone!!

 

You can follow et Al. on The Twitter @lopsidedlablife

Top 20 Pick of the Sci-Pops

Why, it’s….Duran….Duran !

 

Greetings Pop Pickers!! Welcome to ‘Pick of the Sci-Pops’…. your favourite Rock & Pop groups and songs re-imagined as Humungous Hits direct from the Lab bench

Off we go then peeps…..hold on to your tips…because just ejected into the Top 20 are – at 20,

Gladys Knight and the (filter) Tips….

At 19…..are you ‘In Too Deep’, or wandering in a ‘Land of [scientific] Confusion’ – yes! It’s (muta)Genesis

New entry at 18 ….it’s Sir Paul McCartney with his ‘Wings’ pals…lab coats on…running a gel…

……‘Band on the Run’…..(150V for 45 mins should do it!)

Band(s) on the Run

 

Up two places at 17 – the ‘Pocket Pipette of the Prep room’….Yes! it’s Prince and he’s grinding and mincing up the lab with

‘Little Red Cuvette’

Little Red Corvette?…No ! round these parts it’s a ‘Little Red Cuvette’

 

Is your life the pursuit of the perfect Western blot?….. then surely you’re a fan of West(ern) Life….Southern blots giving you the jips? The Beautiful South(ern) should be on your lips…Racing Nicely Alongside these two are the The Verve with ‘A Northern (blot) Soul’….that’s us up to 16 on your Pick of the Sci-Pops, folks!

Staying put at numbers 15 and 14 …..we have two classics

At 15, ‘All Shook Up’ (37oC for 30 mins)….from Elvis and here’s another hero of mine – at 14…yes, it’s Bowie! with ‘Gene Gene-y’

Stay with me Pop Pickers…..straight in at number 13 ….it’s not a re-mix, it’s a ‘Mullis Master Mix’….it’s

‘(Polymerase) Chain Reaction’ from DiaNA Ross

…”it really, really could happen…yes, it really, really could happen” (…manuscript accepted for publication) – staying put at number at 12 it’s Blur! with

‘The Universal’

Your eyes don’t deceive you – this really is happening – The Universal

 

Let’s see if you can ‘digest’ this peeps – at 11 it’s ‘Bam(HI) rap!’ from Wham…

Echo and The Bunnymen??? NO!!! it’s EcoRI and The Bunnymen with their moody classic ‘The Cutter’ – that’s zoomed up the chart to number 10 – I mean lets be ‘blunt’ those last two are bound to ‘sticky overhang’ for a while…

Ok folks, next a Top Science fact …little did you know that Roy Orbison was partial to running SDS-PAGE gels….yup, this inspired this all time classic ……and positively charging into the charts at number 9, it’s ‘Only the Laemmli’

Number 8…..Salsa, merengue…. ‘The Lambada’??? No – in the lab we do ‘The Lambda’…don’t worry – its just a ‘phage’ we’re going through….

This weeks ‘significant’ new entry (p<0.05)…at 7 it’s The Average (+/-S.E.M.) White Band closely followed at number 6 with The Three Degrees (of freedom)

Next – at 5 – a band who came in third in the 2010 X-Factor….sorry Sigma-Factor competition….yes, young ‘uns, it’s (PLoS) One Direction!!!

And on the subject of the next generation… a non-mover at number 4, it’s a 70’s band updated for the –omics generation…..yup…it’s The New (RNA-) seq-ers….

Into the this weeks Top 3…drum roll….drum roll…

At 3…McFly…..Busted……McBusted? What happens when you cross 80’s synth pop cell biologists Soft Cell with 70’s post-punk heavyweights Joy Division… …yup Pickers…. it’s Soft Cell (Division)

Staying in the 80’s, and flying the flag for Moshing Microbiologists – at Number 2 it’s The Cult(ure)…or for synth-biologists – it’s 80’s synth-poppers Culture Club

That us reached the tip of the rack pickers…who has earned the Platinum Taq?….at number one….The album covers were printed wrongly…..they’re big lovers of lab glassware…..yes Pop Pickers….its Duran Duran!! With their classic album ‘Bio’

That’s it folks, hope you’ve enjoyed this weeks run-down of all you favourite science inspired Rock ‘n Pop classics….just who will make an ‘impact’ on the charts next time around?!

20 Gladys Knight and the (filter) Tips

19 (muta)Genesis

18 ‘Band on the Run’ Wings

17 ‘Little Red Cuvette’ Prince

16 West(ern) Life…The Beautiful South(ern)…‘A Northern (blot) Soul’ The Verve

15 ‘All Shook Up’ (37oC for 30 mins) Elvis Presley

14 ‘Gene Gene-y’ David Bowie

13 ‘(Polymerase) Chain Reaction’ DiaNA Ross

12 ‘The Universal’ Blur

11 ‘Bam(HI) rap!’ Wham

10 ‘The Cutter’ EcoRI and The Bunnymen

9 ‘Only the Laemmli’ Roy Orbison

8 The Lambda (Phage mix)

7 The Average (+/-S.E.M.) White Band

6 The Three Degrees (of freedom)

5 (PLoS) One Direction

4 The New (RNA-)seq-ers

3 Soft Cell (Division)

2 The Cult(ure)….and Culture Club

1 ‘Bio’ Duran Duran

 

You can follow et Al. on The Twitter @lopsidedlablife

Used Tips – ‘nearly career’

Used Tips – ‘parents’

Used Tips – ‘Watson’