Friday, 14 December 2012

Science Songs

Finished for Christmas!  Working with flies always makes for a tricky wind-down as you need to time things properly for coming back. It's a frustrating week though when you can only do immediate things, so I'm happy to be done.
I think this song is quite apt.

Thursday, 6 December 2012

Dog Driving School

Maybe a tenuous link to Biology but it is demonstrating how intelligent dogs can be and it does have DOGS DRIVING CARS!!!
The pose of the dog while driving is by far the best thing. Doesn't matter how bad your driving is as long as you look good.

The dog would truly become man's best friend if he could drive you home from the pub after a few drinks. Although the carnage that could occur when a dog is in heat is quite scary. Would the dogs rival white van drivers in their attempts to sniff other car's exhaust pipes?

Saturday, 17 November 2012

Science Songs (mature content)

The following rant contains immature content so for those who blush easily at the discussion of sex and related bodily functions should read on at their own risk. This article also contains terrible pop music so for those with impeccable taste, please don't click on the video.

X-factor winning "little Mix" try their hand at a song about d-d-d-DNA (maybe a misplaced reference to Sanger's dd DNA sequencing?). Anyway I'll let you enjoy the song/video before trying to dissect the lyrics.

And now to look at the lyrics; First verse is just fluff - nothing to do with biology other than being horny. Snide comments are in brackets and not to be confused with bizarre background pop echo lyrics.

"It's the blue in his eyes that helps me see the future  [true on the eyes - not so much seeing the future]
Fingerprints that leave me covered for days, yeah yeah  [I guess there might be DNA from the grooves?]
Now I don't have any first degree  [that's becoming self-evident]
But I know, what he does to me
No need to work it out, it's so familiar  [this isn't a very scientific attitude]"

" And my heart won't beat again
If I can't feel him in my veins  [I have no idea what kinky kind of things they are getting up to - or they may just be sharing needles]
No need to question, I already know  [again with the anti-science stance]"

" He's from a different strain
That science can't explain"
 [Again, I'm sure with the right kind of experimentation and samples, science probably could eventually explain this. Not that it would be a good use of research funding. ]

My favourite lyric by far is this one though;

"It's simple genetic
I'm the x to his y"

Let's ignore the dropping of the "s" (this is maybe how the cool kids use the word) but consider the genetic(s) of the statement. So, the girl is the guy's mum? That's just sick. A pop song about incest. Game of Thrones and Boardwalk Empire have really become a trend setters. The lyrics tend to fit the "pop song innuendo" a lot better if the "DNA" they are referring to is sperm. This may also let them off the hook for the incest line in that she's maybe singing about making a baby, which is possibly connecting with their target audience.

" It's in his dna
And he just takes my breath away
B-b-breath away
I feel it every day, and that's what makes a man"

and "Contaminates my lips"  [she should have read the COSHH form and at least had safety glasses on]

Laying it on a bit thick there? (innuendo intended)

In summary, while it's nice that biological terms are so well known they can be used as the basis of a pop song, it's clear they don't know much about how the things actually work. Or they do but prefer nonsense pop lyrics over substance, which is fair enough. Or they are trying to make the next generation comfortable with the idea of incest.

Wednesday, 31 October 2012

Name the Biologist - Halloween edition

Time for some scary biologists - can you name them?

And this guy isn't a biologist but I'd definitely enjoy being able to study him - after taking all the appropriate risk assessments.

And finally, he doesn't scare me but I think he terrifies certain demographics...

Tuesday, 23 October 2012

Reference Rage!

I've been doing some mutant hunting today for some genes of potential interest and because they are fly mutants it's useful to know exactly what the mutation is as they can range from the gene being deleted, a portion being deleted or have a transposable element stuck in them - all of which effects how much of a "mutant" they are. This information is usually in a figure but sometimes, in a busy manuscript, it will be mentioned in the materials and methods. In this case the mutant was referenced as being described in another paper. Fair enough, I thought, and dutifully looked up the other paper. I scour this paper and it merely says "as has been previously described". Not in the paper, so where? In one of their previous papers? In someone else's paper?

This annoys me as I shouldn't have to waste my time chasing up dead-ends. It wouldn't be so bad if this was the first time it's happened but this is a frequent problem when you are trying to find out the exact nature of a mutant, clone construct or methodology. I don't mind them referencing the original paper if it has all the details but people who reference papers that only reference the source material again should hit over the head with a rolled up journal. It's really bad form and strikes of laziness or, worse, hints the author never actually checked the data in the original source.

If editors/reviewers can't be bothered to weed this reference riddles out, then journals should perhaps insist that the information for mutants etc be included as supplementary material - that way they'd have to cite the original if they are printing their data.

I guess the small mercy is that I at least have access to online databases. This kind of nonsense must have resulted in a lot of premature baldness back in the days when people had to go to the library to find papers.

Monday, 22 October 2012

Science Songs

A song that lends itself to many an occasion, particularly student clubs. I've noticed at science retreats this song always gets a strong response and upon reflection it makes complete sense.

"we've got to hold on to what we've got
Cause it doesn't make a difference
If we make it or not....
...We'll give it a shot"

The chorus reminds me of the PI - postdoc/ postdoc - student relationship of getting them to finish the project.

" Whooah, we're half way there
Livin on a prayer
Take my hand and we'll make it - I swear "

It ahould be an anthem to research!

Sometimes you just need an excuse to play this song :)

Tuesday, 16 October 2012

Wall of Shame

My group leader told a fun anecdote that I think deserves to be a "wall of shame" entry. He was recounting a tale of a student whose experiment kept failing despite their insistence they were following the protocol correctly. He asked they student whether they were getting the correct pH for one of the solutions and the student was insistent they were doing this correctly. Eventually he asked to see how they were pH-ing the solution and the student took him to the pH meter inserted the meter into the solution and then turned the calibration dial to the pH they desired. "Then I turn the dial to the pH I want and it's done", proclaimed the student...

A fundamental misunderstanding of how a pH meter works but an excellent idea for creating a pH-ing machine. I'd love to put a solution into a machine and turn a dial to a desired pH which would in turn convert my solution into the selected pH.

biological Interlude - What happened before the Big Bang?

It seems strange for my first post in a while (been constantly ill in some form or other of late) to be about cosmology but my mind was quite literally blown by it so I thought I'd draw peoples attention to it. For anyone with access to the BBC iplayer I'd urge you to check out one of their documentaries under the "horizon" umbrella asking "What happened before the Big Bang?".

Initially I thought it was a nonsense question as my preconception was that there couldn't be anything before the Big Bang because that's where everything started, including time. Turns out this theory is being challenged by many new ideas which think if the Big Bang even happened, it's either a cyclical event or something that occurred in a previous universe. It turns out it's quite a fertile time for alternative theories and the documentary gives each theory 5-10 minutes explaining the pros and cons. It's refreshing that the show allows the other cosmologists to comment on rivalling theories and it's fun to see how each one is convinced the others are seriously flawed.

After introducing the different theories, several of which overlap the show spends its remaining time looking at evidence that can back up, or more importantly disprove some of these theories. It's nice that the show spends some time to show this aspect of science as there's sometimes a tendency to present all these "out-there" theories as if they are accepted fact and this segment shows that these are all theories as of yet. In an attempt to draw a comparison to Biology, I think all these conflicting ideas mimic evolution in the sense that the strongest one will ultimately survive but i guess science as a whole has always been in service of natural selection in one way or other.

What was my favourite theory? I did like the idea of Big Bangs originating from a Black hole in another universe as it seemed to philosophically get round that whole "infinitely small/dense" problem. I also liked the cyclical arguments of either the universe condensing back in on itself until gravity becomes a repulsive force and the Big Bang is more a Big Bounce (Param Singh) or the similar argument that the end of the universe would actually mirror the environment before the Big Bang and therefore be fertile ground for another one (Roger Penrose). I wasn't so keen on the "Brane theory" (Neil Turok) largely because i couldn't wrap my head around it and it sounded too much like a fairy tale to a lay person like myself (although it makes excellent Sci-fi imagery). There was also a theory at the end that the shows makers and discover (Laura Mersini-Houghton) claimed worked perfectly with the mathematics in that it allowed there to be something from nothing as well as explained three observational findings in cosmology that are currently hard to explain using other models. Unfortunately I had to take their word on that as it wasn't explained why it worked. I imagine it was probably one of those things that couldn't be easily explained in a couple of minutes.

A great little documentary that ignited my imagination that took time to present multiple arguments and suggest ongoing experiments that may help prove which one (if any) is correct. The scientist's in the show all did a great job of getting across the point that even if they are wrong it's good to generate these theories to push the field forward. I was left with one remaining question though and that is whether hardcore mathematicians/physicists really do spend all day scribbling things down on a blackboard?

Thursday, 13 September 2012

Wall of Shame

This one isn't me but is courtesy of a lab mate this week.

They were expressing concern of not seeing any bands in their DNA gels and in an attempt to troubleshoot asked me if I'd had any problems. Other than "shit" results and slightly faint bands (from having changed the running buffer) I couldn't really help. Labmate pointed out he couldn't see the DNA ladder either.

This happened a total of three times. I asked if they had solved their problem yesterday and they replied,

"it's fixed".

"What was up?"

"someone had swapped the gel tank around so I ran the gel in the wrong direction"

They crossed the beams :)

I told them not to worry, I tried to run a DNA gel with water rather than running buffer once and my solution when the loading dye refused to move was to crank up the voltage. I almost managed to set fire to water...

EDIT: Only noticed I'd titled this "Wal of shame". Oh, the irony.

Tuesday, 11 September 2012

spot the difference

The sample on the left right is supposed to be the same as the one on the left. As you can see it is a nice orange colour and no longer transparent despite having not being opened. a colleague pointed this out to the company and while they were happy to refund us they wanted photographic evidence. I'm not sure how rife "media fraud" is within academia but found it quaint how they wanted a photo. So this is what they got. Maybe we should have had a current paper in the background too?

Name the Biologist - week 22

This week should technically be called, "Name the scientist" as he wasn't a biologist. I'm including him though as I read an article on the news claiming he's largely unknown and I don't think that's true. Maybe he's only well known in Science circles or maybe it's just me being drawn to larger than life scientists. Let's see.

As for last week's "genuine" Biologists they were

Monday, 3 September 2012

wall of shame

On Wednesday I tried a transformation which should place mygene-GFP into a plasmid that allows me to make a virus that will eventually allow me to infect and stably express mygene-GFP in cell lines.
I checked it on Thursday and it didn't appear to have worked. In these cases I usually leave them for a few more hours in the desperate (but often worthwhile) hope some colonies will start to appear. The problem was I forgot and I was then away until Monday. Checked them this morning and found there still wasn't anything - although by that point I'd have probably had a plate singing songs from "Joseph and his technicoloured Germcoat".
My response to this was to repeat the experiment again and to check the gel excision for mygene-GFP had actually worked. Then my Padawan student co-worker asked if I'd maybe used the wring antibiotic. "No, it was definitely Kanomycin", I proclaimed. The student replied "but all the viral vectors are ampicillin resistant".
"In that case I've just conclusively shown they can't grow on Ampicillin plates"

I'm deciding to believe that it was the antibiotics that have been in my bloodstream for the last week that was responsible for this work-related antibiotic gaff...

Name the biologist week 21

This week is a bit trickier in that there are 3 biologists to name and a bonus point for what links them. Let's dive straight into it.

Oh and this guy (he pops up a fair bit - definitely not a one trick pony)

That should probably help you on your way.

As for last week, the answer was Craig Venter. Probably best known for setting up a rival to the Human Genome Project in the form of Celera Genomics using "shotgun sequencing". Interestingly, his genome was one of the 5 sample genomes used by Celera for sequencing the human genome. While many claimed the clone approach was more accurate, the competition spurred on the Human Genome Project and Shotgun sequencing has been used for other genomes during and since.
Currently he is best known for his work on synthetic biology in the form of the J Craig Venter Institute, which has some fascinating ideas as well as opening up the idea of owning "life-forms".

Saturday, 25 August 2012

Name the Biologist - Week 20

No clues this week as he should be fairly recognisable.

As for last week's entry it was none other than Joseph Priestley - a fascinating individual whose observations that air could be "injured" by a burning candle and a mouse and "healed" by a plant was the forst step to understanding photosynthesis and respiration. He actually made a whole load of other discoveries such as oxygen and possibly his greatest contrbution was the invention of Soda water and the eraser.

Biologist point-of-view review: Prometheus

Oh dear - what a mess.

Friday, 24 August 2012

Hunterian Museum

I worked next door to this place and never managed to visit the Hunterian museum in London. It's almost worth just to see inside the Royal College of Surgeons' building to be honest. The collection consists mainly of John Hunter's personal collection of organs and specimens in formaldehyde/alcohol from insects through to human foetuses. To be honest the sheer number of glass jars is overwhelming but there are some very interesting specimens and it was clear that he was driving at something with his dissections - often looking at the similarities in organs throughout species.
The history of Hunter and his contribution to the field of surgery is also fascinating. I wasn't even aware that you didn't requite a medical degree to be a surgeon during his time and it was something you learned via apprenticeship. I guess this is because the profession was very similar to that of a butcher at that time. Fortunately, Hunter was a surgeon who applied scientific method to his work and, along with other similar thinkers, the profession of surgery was transformed.
The upper floor has an interesting history of surgery and it's quite amazing how far things have progressed. It's also quite terrifying how painful and deadly surgery was back then and how we really take things for granted. That said by looking at the history of surgery up to modern techniques, I'm sure people a century from now will look on our surgical/medical practices and think we were barbaric.

It's definitely worth a look but be warned it's not for the squeamish!

Sunday, 19 August 2012

Name the Biologist - Week 19

Inspired by two days of Sun, I decided to make this week's entry this guy;

To be fair he is perhaps best known as a chemist. However he made observations that led to the discovery of one of life's essential chemical reactions. Reading up on the guy reveals a fascinating history. He also invented a very popular type of drink and a whole host of other things. A good old fashioned scientist - the type that should still be encouraged still but unfortunately can't due to academic structure almost selecting against it.

As for last week's biologist, it was none other than Galen. It's hard to convey his importance in terms of his impact on physiology and anatomy. Equally important was that he was one of the earliest examples of applying scientific method (Observation, theory and experimentation) to biology and published a work on how the "best physician is also a philosopher". Galen also pretty much came up with the concept of model organisms in terms of dissection and vivisection of pigs and primates to understand human anatomy because dissection was outlawed in Rome at the time.
He also made groundbreaking and lasting discoveries in neurology and established that the brain and central nervous system control motor function. He also described the function of agonists and antagonists on nerves so was a very early pharmacologist.
He was also a damn good surgeon (probably because he practised on animals) and could even remove cataracts! Sadly a lot of his techniques were forgotten for several hundred years. Good proof that his observations on diet and hygiene is the fact that he lived until the age of 87 which is pretty good going for someone in the second century.

Wednesday, 15 August 2012

Science songs

This is the official London olympics song by Muse. Pretty scary in that it sounds like it should be the national anthem of some "300" style nation that has ordered Queen to compose at gunpoint. The reason I'm including the song is because for some unknown reason they have people chanting "somites" throughout it. I heard a lot about somites in relation to Zebrafish. If I ever hear any other talks about somites this song will play in my head.


Edit: For some reason Youtube will only let you watch the video through their website. I'm sure you know how to click on it though.

Tuesday, 14 August 2012

Name the Biologist- week 18

This guy is from way back. Wiki doesn't call him a biologist but I'm willing to argue that he is.

As for the previous edition's answer;

Sunday, 5 August 2012

Biologist point-of-view review; Dark Knight Rises

A more than satisfactory conclusion to the Batman trilogy, this franchise has largely dodged biology, possibly because they were avoiding any "super" people. I'm sure physicists and engineers may have a few issues with the science though - even my head hurts at the "it's cool but how could that work" spinning wheels of the bat-bike.
The only thing I can comment on is the view of how academic publishing works in the world of "Batman". Don't read any further if you want to avoid spoilers.

So there is a physicist who apparently publishes a paper on how to turn a fusion reactor into a bomb. It's pretty impressive considering no-one has built a fusion reactor (except for Bruce Wayne who then shelves the project because of the paper). Let's say the guy published a paper on the theory of how to do this. Well, the villain, Bane, goes to great lengths to capture this scientist and it makes for quite the spectacle when he informs the citizens of Gotham that this is the only person who knows how to make the bomb, which is now armed. He then kills the scientist - implying there is no hope. The problem with this is that if the guy published a paper on how to make a fusion bomb then by definition he should have detailed how one could be made. In terms of peer review a key criteria for a paper being published is that others can replicate the results. This should mean that any decent physicist should also be able to make a bomb. 
In fairness maybe the scientist never published his paper on how to theoretically disarm a fusion bomb in which case he would be the only person who would know how to do so (or it would take a while for others to figure it out). The lesson here, therefore, is that you should publish your results as quickly as possible, nevermind the threat of being scooped - their may be an odd-voiced terrorist super-villain wanting to use your work. At least once published there's no need for them to kill you to keep your work a secret.

Name the biologist - week 17

I've been struck by olympics fever so this edition is inspired by it.
Unfortunately, this seems to be another case of "there aren't any pictures of the people involved". Therefore you will have to make do with the ones involved in the process and guess the theme. I'll mention the other biologists when I give you the answer in the next installment. This guy definitely got the ball rolling though.

And this guy was pretty key in coming up with a theory for how it works.
Finally, this guy got to the root or the actual chemistry of how the whole thing works.

What's interesting is how it took a hundred years and research by several different researchers to get to the bottom of how this thing functioned. That's science for you; a long distance relay event.

The answer to the last installment was Frederick Sanger who developed the DNA sequencing method that used dideoxy chain termination. This method is still used to this day and it was instrumental in completing the human genome and Fred himself was one of the first people to complete a genome when he sequenced the virus Phage Φ-X174. In honour of his contribution to sequencing an institute in Hinxton was named after him as the Sanger Institute which is one of the world's leading centres for genomic-based research. He's also one of only a handful of people to have won two Nobel prizes.

Thursday, 2 August 2012

Pearson's test

In my new job, they take co-localisation and linked increase/decrease in signal very seriously so the Pearson's test is mentioned a lot. This confuses me as I always think they are talking about me and is particularly worrying when I am drifting out of a talk.
Sadly I didn't invent the formula bit sometimes I wonder what I would have created it for?

Tuesday, 31 July 2012

Biologist Point-of-view-review: Amazing Spider-man

As you may have gathered from some of my other posts I'm a bit of a comic-geek. I thought this would be a good place to do some reviews of films with "biology" in them and the "amazing spider-man" is a good place to start.

The film is good, solid fun. It makes some welcome changes to the previous films and Andrew Garfield is inspired casting. My main focus is on the biology presented in the film and in order to discuss that there will be some spoilers with regards to the film's plot. So I wouldn't read any further if you don't like spoilers.

Name the Biologist - "week" 16

Sorry for the tardiness. A busy couple of weekends has prevented me from doing the feature justice. Luckily "anonymous" is good at getting these right so hopefully people weren't pulling their hair out trying to discover the answer.

This one should be realtively easy. I will try and make the next one more of a challenge.
As for last week, from top to bottom we have Theodor Boveri, Walter Sutton and Walther Flemming. Boveri and Sutton are famous for working out that the chromosomes are the carriers of genetic material. this is one of those things we take for granted now but it was a major breakthrough for linking genetic theory with molecular biology. Case in point is Walther Flemming, the scientist who first described chromosomes but because he was unaware (of the then lost) work by Mendel never quite realised just how important his observations were.

Saturday, 7 July 2012

You couldn't make it up

This video explains the utterly bizarre mating process of the Angler fish. Nature is utterly bizarre. EDIT: as is my use of the same description twice in a row.

The ultimate clingy boyfriend or a metaphor for marriage?

Name the Biologist - Week 15

Busy couple of week meant I was a bit slow at finding a new candidate. But I've managed to dig up another one continuing the historical theme.

The sizes don't really reflect their relative importance. As a little bonus this guy should also be included although he didn't come up with the importance of what he found.

Although he wins in terms of owning the facial hair contest.

As for the previous edition, which was "off the hooke" it was none other than Robert Hooke, the scientist who coined the phrase "cell". He was one of those super scientists in that he wasn't content with describing and coining the word "cell" but also described a physical law too. He also wasn't that far off working out gravity and he made his own microscopes so he could draw small creatures. Basically if he was around today he'd put a dozen different types of postdocs out of work. I'm jealous as I'm more likely to break a law than have one named after me.

Science Songs

My PhD was in spindle formation and how the centrosome isn't essential, so you can forgive me for thinking this songs has the lyrics "End of the Centriole. It's nothing special"  You'd have to work on the subject to appreciate it, I guess...

Stat's more like it

Brian Cox lays down an inconvenient truth about the banking crisis and science,

The jury is out on whether mentioning Jesus is a good call but the gist of his point is mind boggling. It's one of his favourite stats and he explains it in more detail at his lectures.

As for him getting into politics, I'd probably vote for him but I'd want Jim al-khalili as his deputy prime-minister and Dawkins as the background politician that winds voters up.

Saturday, 30 June 2012

Science Songs

For anyone who has ever conducted a screen in science, I don't need to say any more...

Thursday, 28 June 2012

Marvelous Scientists!

I stumbled upon this list today which compiles all of the scientists that have featured in the Marvel Universe. I have to agree that Marvel comics has a pretty favourable view of scientists and celebrates them. Pretty much all of their major characters are scientists; Mr Fantastic (that super smart PI), Iron Man (sell-out to industry), The Hulk (postdoc too many) and Spider-man (who is probably the most student/young postdoc- relatable). It's nice that they have this as part of what makes them a hero too and in many cases it's their science that gets them out of trouble (although it's always good to throw a few punches in there too).

Monday, 25 June 2012

Name the biologist - week 14

Here's another old one - so old it's a painting rather than a photograph. I guess that could be a clue in itself. This guy named something that's pretty essential in biology.

As for last week they were the biologists who came up with the one gene-one enzyme hypothesis. George Beadle and Edward Tatum.

Thursday, 21 June 2012

Science Songs

I'm sure this song was supposed to be about losing a girl but I was listening to it yesterday and it reminds me a lot of science and getting a PhD or paper. Bear with me and listen carefully...

Monday, 18 June 2012

science pun!

I stumbled upon this image and pun today. I will definitely find opportunities to use the phrase "Drosoph-apocalypse" in the future. Sadly it will probably mean something horribly wrong has happened.

Name the Bioblogist - week 13

So there was a week long absence due to football being a bit busy and uninspired but I've manage to come up with a new one. This is an old school one so I will give you a clue, these two came up with a fairly important hypothesis in genetics/biochemistry.

As for the last installment, "Anonymous" wins again by recognising Elizabeth Blackburn, Carol Greider and Alexey Olovnikov. In hindsight I should have also included Jack W Szostak too. Anyway they get a mention for their work on Telomerase the enzyme that adds DNA repeats onto telomeres, the ends of chromosomes in vertebrates. It's also been linked to cell ageing which wins it a lot of attention (and is often used as a magic ageing up of human clones in sc-fi)

Friday, 8 June 2012


I was thrown off balance today when my PCRs worked. My plan for the afternoon was to start from scratch with new dNTPs, frsh DNA preparation etc so I had to quickly figure out what to do next. The answer turned out to be more PCRs as i need more of the product to do the digestions afterwards.

This puts the KO method ever-so-slightly ahead of the P-element excision. Then again it is possible that I could cross my isogenised (in bred) P-element flies to the transposase next Friday.

Thursday, 7 June 2012

Well travelled flies

I had a gig to attend work-related fly retrieval mission yesterday for a student in the lab. My old lab had a mutant he needs, so I selflessly decided to go and get them for him.

Monday, 4 June 2012

The chances of anything coming from Mars are 0.70 (or 0.59) they said

Sorry to those of you without access to the BBC but i'm sure it's accessible elsewhere on the net but this list of "Planets most likely to have or sustain life" was pretty interesting. The actual paper is in the journal of Astrobiology but it's a subscription journal (boo) but i will see if my uni has access to it as i'd like to read the actual paper. Anyway it comes up with two criteria; the Earth Similarity Index and the Planet habitability Index.

Sunday, 3 June 2012

Place your bets please!

A big part of my new project is to generate a null mutant of two genes in Drosophila to see what effect they have. My hope is that it kills them or has some nice developmental phenotype I can then dissect further- we have proteomics, from human cells, suggesting this should be the case.

So the reason we make a mutant is fairly straight-forward. If you take a gene away and something goes wrong then you can claim that gene is required to prevent those things going wrong or more accurately you can infer what the gene is required for in a normal situation. There are basically 3 ways you can make a mutant in flies.

Name the Biologist - Week 12

This week i'm doing a few mug shots as they are all connected. You can guess the connection and if you're really smart name them too. So here we go

A) this guy had the hypothesis;

B) And these two helped prove it by finding a key component;

As for last week's answer it was no other than Hans Adolf Krebs of "the Krebs Cycle" fame. I told you he was someone most high school Biology students will have encountered or cursed at some point in their lives. Although once memorised, that was a gift of an exam question.

Wednesday, 30 May 2012

Clone Wars

Part of the reason I took the new postdoc position was because I knew my general cloning skills and biochemistry were a weak point. I think Achilles heel wouldn't be an exaggeration of late!

Monday, 28 May 2012

Name the Biologist - week 11

This week I'm putting up a mug shot that anyone who tackled higher biology at school will have no doubt encountered. Anyone who's done an "A level" or a biology degree will have had to memorise something because of this guy!

As for last week's mystery biologist, not even "anonymous" got it which means it was either difficult or he/she couldn't be bothered this week. It was Edwin Summer - inventor of the Southern blot and inspiration of its compass based spin-offs.


A colleague of mine discovered one of the freezer doors in the lab was open on Saturday and everything had defrosted. It's the freezer right next to me so I instantly felt guilty because it's right next to me and I use it a lot. It is however a communal freezer and I left quite early on Friday so live in the hope it wasn't me. That said, I was in work today, determined to be extra vigilant of the freezer not being shut properly, partly so I could tell if I was the culprit or not. So I opened the freezer and was surprised when the door came off its hinges.

Monday, 21 May 2012

Name the Biologist - week 10

Sticking with a theme at the moment, here is this week's mystery biologist.

Update: This one seems to be causing problems/lack of interest, maybe I should try and point you all in the right direction?

As for last week, the answer is behind my newly discovered spoiler text (do i have to explain how it works?). Carey Mulligan Kary Mullis the developer of the polymerase chain reaction (PCR) an absoultely essentially, if sometimes black art, for pretty much every biologist. Kary definitely seems to be a character if his views on AIDS, LSD and climtate change are any indication and I've been informed that his autobiography is a very entertaining read. Probably worth checking out.

Monday, 14 May 2012

Name the biologist - week 9

For people who've heard my frustrations at work (which I know I promised to update on the blog but haven't got round to yet) may be able to make a guess as to who this weeks mystery biologist is.

Sunday, 13 May 2012

The Great Gummi Bear Experiment

What follows is the hard work of some co-workers from my old institute. 

Gummi bears expand when soaked in water

Abstract: Food items that get caught in the throat are a common cause of concern and irritation. It can often lead to worries of esophageal cancer or cause restriction of breathing. "Sticky" foods can stick to the back or roof of the mouth and Gummi bears are particularly hazardous. Cases of "gummed up throats" (GUT) usually occur in young children or adolescents and have been known, in extreme cases, to become stuck in a person's throat for 2 weeks (citation needed). Here we investigate and validate the claim that Gummi bears are made more dangerous due to their ability to expand when soaked in water. This research also shows that while gummi bears expand over 48hrs their structural integrity causes them to shrink after this point - offering hope to sufferers of GUT.

Tuesday, 8 May 2012

Alternative Medicine Fail - Pills made from baby remains

I just read this link. I emphasise link as I don't read the Daily Mail - unless it's for a better understanding of science scare mongering. First of all, I can only hope that it is Daily Mail scare mongering and not 100% accurate as it's pretty shocking and disgusting that such a practice is going on.

Sunday, 6 May 2012

Name the Biologist - Week 8

This week is a somewhat sad entry in the sense it shows not everything works out in science. The irony being this guy makes up for at least 90% of all biologist's careers so it's good to hear their stories too. I imagine some people wont even need the picture after that introduction but here goes;

As for the identity of the previous name the biologist...

Saturday, 5 May 2012

Science Songs: RIP Adam Yauch

I was wanting to post this one a while back but due to EMI policing their copyright it's impossible to get the song off the net (well, without very intensive searching). Sadly Adam Yauch, of the Beastie boys passed away to cancer yesterday. Everyone should like at least one Beastie Boys track as they had a huge range. But they had a song called "the sounds of science (and an entire anthology bearing the name) which fits this feature perfectly. I urge you to track it down on Spotify or something, Until then we'll have to make do with the lyrics.

Tuesday, 1 May 2012

Name the Biologist - week 7

This is one that a lot of Edinburgh PhD students should know.

As for last week's scientist.....

Monday, 30 April 2012

Science Songs

"Chemistry" by Semisonic. There are a lot of Biologists who would agree with the chorus "it's all about chemistry".

Saturday, 28 April 2012

Caught read-genomed

Here's me having a pop at writing about some actual science - yeah it does happen every now and then.

With the advent of cheap, high throughput sequencing it’s only a matter of time before we all have our personal genomes, all three billion base pairs of it, at our disposal. It’s fairly obvious how having our own genome sequenced can, and will, revolutionise medicine from personalised drug treatment to identification of a whole host of risk factors in disease. There are other far-reaching and seemingly far-fetched uses for our genomes though. One area that may see some of the biggest advances is in the world of forensics.

Thursday, 26 April 2012

Everything on a sliding scale

My friend, Maxine, did me a huge favour by sharing this link  from the smallest thing known to man to the largest observable thing known to man this webpage is as awe-inspiring as it is vertigo-inducing. Honestly my head hurts from the experience but in a really good way.
I tend to stick to biology and there is a "small" portion of it that includes it but sometimes it's ok to make an exception and this is definitely worthy of it.
Enjoy! I'll put my favourite bits under the "read more" tag so you can discover your own surprises. If you come straight to the full article then DON'T read what follows until you've been to the website.

Wednesday, 25 April 2012

Science erotica

I had to order some plastic pestles for squashing flies in test tubes today as people were trying to make do with pipette tips and I was all "I can't work in these conditions" diva-ish about it. So i tried to find out how to obtain these essential items - well I just asked a friend if she could tell me how to obtain them. Ever reliable my friend soon emailed a catalogue link where we can now all bask in the glory of said pestles.

Sunday, 22 April 2012

Name the biologist - week 6

The last one proved a bit tricky so this one should be easier. The guy was one of those folk who didn't just stick to biology - show off.

As for last week's Biologist:

Tuesday, 17 April 2012

Odd journal covers

This is an eye-catching cover for the latest issue of "Developmental Cell".

It has a really strong "Flash Gordon" pulp sci-fi vibe. Still, I have to admit surprise at them going for such a fantastical image - it doesn't exactly scream accurate. I wonder if there was a last minute change of cover? Or did they expect "john carter" to have been a bigger success? I'm not sure how i'd feel if i had a paper on the subject the cover is depicting. Well, i'd probably be fine (I'm a geek) and to be honest I'm sure there have been bigger works of fiction made it onto the cover of journals passing itself off as real. Miaow

If my paper ever does get published this is the cover I'd like:

What kind of Cover would you like for your work?

Why we grow ears on mice

The ear on a mouse experiment is pretty infamous for it's use in media and tabloid scare mongering, The sitcom "Community" offers up an alternative reason for why the experiment was done, which is thankfully ironic but i think some people would see it as true.

Sunday, 15 April 2012

Name the Biologist - Week 5

This may be the trickiest one yet...

Update: Here's a clue for those of you who may be lagging behind...

Update 2: Maybe some of you are following the wrong strand?

Friday, 13 April 2012


This has to be one of my favourite science puns!

Well done to the creator who I guess is the name at the bottom of the picture. I tip my hat, to you.

Monday, 9 April 2012

Name the Biologist - week 4

I think this one will be tricky although it really depends on what type of model organism you work with.

Below are the answers to the previous editions.

Captain America - The first Avenger

I'm a big fan of superhero comics. The X-men and Spider-man comics/cartoons probably had a bigger influence on my decision to become a geneticist than I'd care to admit. For that reason I've been enjoying all the Marvel films that have been building up to next month's "The Avengers" film. The film is good fun and it's definitely in the Indiana Jones/The rocketeer mould (the latter of which was also directed by Joe Johnson) although I'd say it was the weakest of the Marvel "universe" films (even the often ignored recent Hulk film).

But why am I mentioning it in the blog?

Saturday, 7 April 2012

Even scientists have birthdays...

The lack of activity is largely due to lack of internet access but I've been busy moving too. It's also my birthday so i'm having an indulgent easter.

Normal schedule should resume in a week.

Sunday, 1 April 2012

Name the biologist special edition

Today is a special day, as you may have gathered from the "endgangered species" post so here is a special edition "name the biologist". Enjoy!

Bonus imaginary points if you can name all 3.

Endangered species

The IUCN (Internatinal Union for Conservation of Nature) red (ironic) list has added "gingers" as a "sub species" that is potentially endangered. To be fair it's in the lowest category of "least concern".
I think that's a first for people as it's not like gingers are a separate species. It's shocking news for me reading this information on a sunny early april morning. What exactly does being added to this list mean for me? Why are gingers dying out and what can be done to save us?

Thursday, 29 March 2012

In Transit

I'm away to find a new home, so will be ignoring the site for the next few days (or being minimalist when I do visit). In the meantime here is an article from the BBC (sorry non-UK folks) that does a nice job of high-lighting why research on flies is worthwhile.
It's a far cry from this would be world leader's view! (the only clip I could find included this rebuttal which I guess adds a bit of context for why Palin's comment was so stupid).

Wednesday, 28 March 2012

Name the Biologist week 3

Here is this week's mystery biologist.

And just in case that's too easy here is a fun spin on the concept. Name the musician/band!  : P

Tuesday, 27 March 2012

Are they on the Y chromosome?

The title gag is just too easy to make regarding this article "Gene flaw linked to serious Flu risk"

The actual paper is quite interesting though as it provides evidence for why some people are more susceptible to flu (and other viruses) than others. The interferon-inducible transmembrane protein, IFTIM, ("catchy" name) This kind of work is useful in that it can highlight "at risk" people for vaccines in much the same way that asthma sufferers are on a priority list. It also shows how it may not be just bad luck that some people seem to be ill more often than not and these kind of studies are likely to only increase the awareness that our genetic background is a vital factor in disease resistance.

Monday, 26 March 2012

Science song

This is another "on the nose" science song, where it's hard not to notice the lyrics. That said, I initially thought the chorus was "karaoke girl" so it shows how much attention I pay.
So here it is; "Biological" by Air.

How did Superman's powers ever evolve?

The explanation for Superman’s powers are one of the more simple ones in comics. He’s an alien from the planet Krypton and that’s why he is super strong, can fly and shoot lasers out of his eyes. Fair enough. You can’t really argue these facts as we don’t know anything about the alien physiology. Where things start to fall apart though is the suggestion that Kryptonians are solar powered – specifically under a yellow sun. The problem with this is that the planet Krypton has a red sun. My question is “how on earth Krypton did Kryptonians evolve to have super powers under a yellow sun?”. 

Friday, 23 March 2012

D.N.A. of a Scientist

Ok, I've been a bit lazy this past week (paper manuscripts, job contracts and genuine laziness) with the blog but here's a feature I'm hoping will take off which is trying to "interview" various scientists. I painstakingly tried to come up with a name and have settled for "Dare Not Ask of a Scientist" as it kind of works on a few levels then.

Science Song

Not the greatest of korn songs but it fits the tenuous bill.

"And I'm sorry that I don't believe
by the evidence that I see
That there's any hope left for me
It's evolution"

Wednesday, 21 March 2012

Name the Biologist - week 2

The last one was accused of being "too easy" - although only one person deemed to try and guess it. It's not like it was Darwin easy! So here's another one. A certain type of biologist should know this one as the guy should be a poster in their bedrooms. So here we go;

Again, first person to post the correct guess wins "bragging" rights. I will put the answer to the last entry under the "read more" tag just in case you are doing the quizzes in the incorrect order.

This one seems to be proving tricky so I'll give you a more recent picture.

Horizon: The truth about fat

I have to admit I've been bad at keeping track of BBC's science documentary show, "Horizon" this year, which is a shame as the previous series was excellent. That said it was on in the background yesterday and I found myself been quite drawn into it.

Science song

This one isn't instantly obvious but again listen carefully. The album name is more obvious.
This one is even more apt when combined with "breaking bad" footage. The song does capture that frustration of experiments and lab life getting out of hand quite well though!

Tuesday, 20 March 2012

No longer between Postdocs!

So, as of next month I'll be back at the bench using my Drosophila skills to try and answer some new questions (or get answers to long-standing questions) regarding endosomal sorting. I'll also get to try my hand at some new techniques such as mammalian cell culture and SILAC (which still sounds like a new villain for Battlestar Galactica) which is always worthwhile. It's also on a fairly different topic from my previous research - although the sincere hope is that this area has a strong role in development (it already does I'm just looking for extras).
I'm quite excited (which is a lot coming from me) and hopefully I can share more details once I get there.

Monday, 19 March 2012

Science Song

I've never really paid attention to the lyrics in this song but it's pretty embarassing that I haven't noticed them before. Song sounds even better now!

Drowning your sorrows

This article in is too good not to comment on and yet another reason why research on fruitflies is brilliant. Their research basically shows that male flies are far more likely to choose a drink with alcohol when they have been sexually rejected. Looks like a conserved behaviour!

Friday, 16 March 2012

Thursday, 15 March 2012

When Presentations Go Wrong...

The Dark Crystal is an excellent film but is also quite disturbing. As a child there was one particular scene that scared the hell out of me. The funny thing is the same scene still scares me, it's just that now it reminds me of a science talk where all the audience (particularly group leaders) decide to tear someone's presentation apart. Trust me, I've seen students/postdocs looking far worse than the Skeksi that is attacked in the clip below. I think I've even heard a group leader use the same phrase at the end...

Wednesday, 14 March 2012

Name the Biologist!

Biology pop quiz! Can you name this famous biologist? I'll put the answer up when I'm back from my interview. There aren't any prizes other than the potentially deep satisfaction of being the first person to guess correctly.

The British Invented DNA!

Today's a lazy day (I'm actually preparing for an interview) so I'm just reposting something from my other blog (when this one was just a twinkle in my eye), which was after watching David Cameron, on the Andrew Marr show, make a pretty bold claim.
Luckily someone has put said clip on youtube.

Science Songs

There's a surprising amount of science that turns up in music, which is nice as it means that it's working it's way into the public mind. Sometimes it's obvious from the title but the best ones are where they sneak a science term into the lyrics. What I'll do on "busy" days is stick up a "Science Song" and you can work out the connection to science. So as not to be accused of making it too easy the first song I'll give you is Red Hot Chili Peppers "This is the place". I think this has a particularly clever use of a biological term and I wonder if a geek has ever tried to use it as a pick-up line?

Tuesday, 13 March 2012

Fevre Dream - George RR Martin

Another shameless plug of one of my favourite authors although this time I'm afraid I'm going to have to pull him up on some nonsensical biology, which put an infuriating tarnish on an otherwise excellent vampire novel.
Fevre dream tells the tale of a 19th centuryvsteamboat journey along the missisippi that acquires some unsavoury mythical guests. The book is actually very good and perfectly blends the feel of the deep south with horror.
One of the things I enjoyed about the book is the authors approach to the vampires in that he treats them as biological creatures rather than fantastical ones. To this end he goes to some interesting lengths to establish them as an off-shoot of humantiy - I won't go into details but half the fun is in discovering his "rules" for vampires.
There is one rule that upsets me though and I guess this is technically a little bit of a spoiler so you probably shouldn't read on from here.


When I was growing up one of the stories that always caught my attention was the "Giant vegetable/fruit/cow" story and the idea that if we could make food bigger it would somehow make it easier to feed the world's growing population. At the time it made sense but now I can't help but think how ridiculous the idea is. I also reckon that we're approaching things from the wrong angle. So here's my idea:

"why don't we make humans smaller?"

Monday, 12 March 2012


This is a vintage silly discussion that came up in my old lab one coffee break but I thought was worth sharing again (Filler material and the blog isn't even a week old!). Identical twins are a topic of discussion that geneticists like to bring up a lot.

Tasmanian Peril

This is something I was completely unaware of until last week; the possibility that Tasmanian Devil's may well become extinct over the next 25-35 years. Even more bizarre is the fact that a transmissible face cancer is the cause.

Friday, 9 March 2012

Game of Thrones

Ok, for my first commentary on science in fiction I'm going for HBO's "Game of Thrones" based upon the amazing "A Song of Ice and Fire" series by George RR Martin. But that's fantasy, I hear you all cry. Well you'd be right but there's still a surprising amount of genetics in it, so much so that it's the key to one of the show's central mysteries.
So what are these tenuous connections with biology that I'm claiming the show features? Well in order to do that I'm probably going to have to spoiler warning the following as it does contain a discussion of plot elements from the series. So be warned if you click on the following and haven't seen the first season of the show there are some big spoilers!!!

Between Postdocs

So I can't really do any "day in the life of a scientist" posts as I'm currently unemployed although a far better way of looking at it is that I'm very carefully considering the options available before choosing the "right" position for me. That's dedication considering I'm forsaking any income while making such noble choices.

Opening a can of worms

Possibly the laziest title for any commentary on a C.elegans paper but why not set a low standard of cliche from the offset?
Here's a paper I found quite interesting the other week that challenges the notion of redundancy in eukaryotes.

Thursday, 8 March 2012



One thing I promised myself, once I started a new postdoc position, was to start writing about Biology more. Well I've finally found a fabled second postdoc position so my excuses have ran out.
I'm not entirely sure what this blog will be about other than a general look at science. I guess the fact that I'm a biologist means it is only fair that I allow a little bit of evolution to take place. Survival of the fittest or things that interest me the most I suspect. My initial plans are to try and do a few regular (a term I suspect will have a very loose definition) features on the following areas:

Bench Press : A journal of my day to day work. I'll try and be as honest as possible about what goes on in a lab, warts and all. I'll even try and tell you what I'm doing - although I'll have to be ever wary that the scoop vultures could circling over me.

Real Science: Not that my science isn't real but I'd like to comment on the stuff that's being published and therefore as "real" as it gets. I'll try my best to keep this as varied as possible and outside my own field.

Silly Science: I'd like to do a "scientific approach" to answering silly questions every now and then. Some Examples will emerge soon that will explain what I mean.

Science Fiction: commentary on science as it appears in all forms of entertainment. Maybe including the odd review.

That should be enough to get me started and hopefully see what works for me and everyone else.