Friday, November 23, 2007

Science Singles: Back once again

Yep, it's back .

Let's see what sciencey pop songs I've missed while I was stuck in a hole writing up.

Kaiser Chiefs - "Love's Not A Competition (but I'm winning)"

Science?: If one takes the rather unromantic and reductionist view that the concept of romantic love is nothing but the complex manifestation of basic mating urges combined with a strong pair bonding instinct, then love is indeed a competition. Many animals compete to win a mate, or to win valuable access to favourable mating grounds. From stag beetles to elephant seals, they're all at it. Zoologists consider the successful males those that have their share of successful copulations with fecund females, resulting in the birth of progeny. Is Ricky Kaiser Chiefs winning? Wikipedia no mention of Ricky Wilson having successfully copulated with a fecund females resulting the birth of progeny. Therefore, this hard boiled Darwinian blog considers him not a winner, but a loser.

What's it like?: When I first heard this I was convinced it was a cover of some 80s tune by Duran Duran or some such (apparently it's not). That should act as all the review you need.

Pendulum - "Granite"

Pendulums are part of a bit of science known as "Physics". This type of science, considered by many to be a dark art practised by black hearted necromancers, is so obtuse and arcane that no mortal can understand its ways without first going mad. The diagram below showing the key components of a pendulum clearly demonstrates this, as each elements sounds as if it belongs in a piece of gritty social realism theatre about life in a 1960s prison rather than a weight swinging about on a piece of string.

What's it like?: Granite is a common type of igneous rock, and this tune most certainly does (rock that is, not igneous. This tune igneouses would make no sense). It manages to achieve sounding great, whilst simultaneously sounding like a late 1990s dance remix of a slightly gothic metal song. Quite how this is done without sounding shite is a mystery only bettered by that of physics. Also there are X-Files-esque aliens in the video, which earns extra geek points and make me slightly scared. Well done.

Sunday, November 11, 2007

Not science but....

I know this isn't science, but xkcd is ace.

Monday, November 05, 2007

An excuse to pompous

This may just be the delirium setting in, but I'm really enjoying writing the discussion of my thesis. I get to write such wonderfully pompous wank as: "I would therefore suggest that initially the cartilage and the ossified process are a highly integrated, but separate pair of developmental units. As development proceeds though to the post natal period, this integration becomes so great that they effectively function as one unit. "

[in a Stephen Fry in Blackadder stylee] baaaaahhh!

I think my typo in the last post was a Freudian slip though. I doomed.

Wednesday, October 31, 2007

T minus 13 days and...

... and actually things are going scarcely well.

I've done the bulk of the writing, having done an rubbish introduction, and four ok results chapters. My figures were pretty much done as I went along, there's no stats to do thanks to my mickey mouse subject (whoop whoop!), and my supervisor is being super helpful in reading what I've done.
All I have to do is write the general discussion, add a few sections to the intro, collate it all in to one document (which doesn't look all that painful), do the references, format the bugger, bind and submit. Hmm, doesn't sound like a small amount now I've put it like that.

It's all been going too well. I'm sure some disaster is about to befall me. Not least from the examinations office, who I have to convince to let me submit before I said I would on all the stupid forms.

Monday, October 22, 2007

How not to go about writing you PhD thesis

I've done what is perhaps a very silly thing. I've accepted a post-doc position which starts on the the 12th of November. It is today the 22nd of October. I have yet to finish my thesis. In truth, I had yet to start writing my thesis in earnest before last Tuesday. It is a condition of my starting the post-doc that I have submitted my thesis.


I've managed to wrangle them to let me start if I've finished the writing, allowing a couple of weeks for proof reading and binding. Over the next three weeks there will be no poorly wirtten things about science, and there won' t be any Science Singles, but there may well be the incomprehensible twitterings of an inceasingly more desparate writing up student.

I'll see you on the other side.

Thursday, October 11, 2007

Big Up Pinball Number Count

Science singles will wait this week, too much writing of thesis to do.
In the mean time I want to big up this to the nth degree.

You need to be able to count to do science. I pretty much learnt to count from this. And it's so funky, it almost funks itself to death.

Wednesday, October 03, 2007

Science Singles

I've just realised that the name for this sounds a bit like a dating service for lab workers... oh well, let's get on with it.

CSS with Alcohol

Science? "Hey hey hey hey hey, do you want to drink some alcohol?" Well, it's 11:30 on a Monday morning, so it's probably not the best time to be getting drunk, but in the name of science and rock'n'roll I will. Ethanol (the alcohol you'd hope to have in your beverages) acts on the brain as a depressant. It decreases the activity of the nervous system by inhibiting (amongst others) the NDMA class of glutamate receptors and GABA receptors. These receptors are important in cognition, memory and motor skills, which is why you become a malcoordinated, forgetful fool after several pints. Mine's a brown ale.
Is it any good?
Its a great pop tune with drunk bunnies in the video. I like good pop tunes. More good pop tunes please. And more drunkbunnies.

Tuesday, September 18, 2007

Facebook and science

Like all the best London based media outlets (ha!), I'm going to go on and on and on about Facebook for a bit (but about a year too late, I really am cutting edge).

Facebook (*sigh*): I think I hate it, but amazingly I find myself a regular user; a fact that makes me sad on the inside. And yet some in the scientific community have taken to it like geeky ducks to nerdtastic water, no doubt a large part due to Facebook's origins as a university/workplace social network tool. There are over 500 science groups on Facebook, and I'm sure some are actually about science, such as the "American Association for the Advancement of Science" groups, and more frivolous ones such as the"I listen to the Guardian Science Podcast" and "Null Hypothesis - the journal of unlikely science" groups.

Now Biomedcentral have the option to post articles published by them on to Facebook (along side social bookmarking sites like digg and cool specialist scientific bookmarking sites like citeulike). I cannot quite work out if I'm angered or amazed by this. I think I'm amazed, it's really great to see social networking and all that web2.0 stuff creeping into biomedical science. The only think that makes me slightly scared is that Facebook is just a passing fad, and in a years time we'll all be like "hey remember Facebook? No one uses Facebook now, all the cool kids use Kidney Network". That said, BMC have nothing to lose in adding Facebook functionality. Who knows, maybe these social networking sites might revolutionise the scientific publication system in ways we are yet to imagine.

This reminds me, I really should add digg,, etc.. this blog.

Monday, September 17, 2007

Science Singles (seriously, ""...) with I got it from my momma (Genetics)

Science? Here's a brief synopsis of the entire lyrical content of this song: "I say my dear, how is it that you have such a pleasingly proportioned body?" "Why, my dear old mother is similarly blessed with a fine figure" "Oh I see. It must an inherited trait. Let's have sex"
The thing is, whilst attractiveness has a genetic element, environment plays a very big role. The lady is chatting to no doubt works out, has a good diet, and (on the strength of the video) has had plastic surgery (maybe her mother paid for it?). And anyway, if it was genetic you've got to take in the father into account too.

Is it any good? It makes me sigh and feel slightly more empty inside.

Kate Nash with Mouthwash

Science? Good oral hygiene is obviously important to Kate "flavour of the month" Nash. She uses both mouthwash and dental floss, which our dentists tell us help prevent periodontal diseases and dental caries. Mouthwashes are often antiseptic and antibacterial, and so are claimed help to reduce the number of plaque-causing bacteria. Similarly, we are told by dentists that flossing is really important in reducing dental caries. However, one recent systematic review suggests that flossing at home is not all that effective.

Is it any good?
Damn you Nash, damn you to hades. Despite my best efforts, I cannot help but find my self warming to Kate Nash's music. It's catchy dammit.

Monday, September 10, 2007

Big Up Science Singles

It's Monday. Let's see what we've got here then....

The big release for me this week is Chemical Brothers with The Salmon Dance

Science? They are called the Chemical Brothers, but that's not all. This song is jam packed with salmon facts, all presented in a handy hip-hop format by Sammy the Salmon:
Fact 1: "All my peeps spend part of their life in fresh water and part of their life in salt water... They change round a couple of days after spawning, then we die."
Indeed, at around 2 years of age, young salmon leave their river habitats and migrate to the sea. They then return to the river after a year or so to spawn. However, they don't then die, instead they go back to the sea and return to the river gain around every 18 months to spawn. I'm disappointed in that factual error Sammy the Salmon.
Fact 2: "Most of our friends find home waters by sense of smell, which is even more key than that of a dog or a bear."
Salmon which were imprinted to Morpholine (C4H9NO), a heterocyclic amine, could detect the chemical at concentrations below 5.7x 10-10 M.
Fact 3: "My family also rely on ocean currents, tides, the gravitational pull of the moon."
There is also a theory that some salmon species can detect the earth's magnetic field.
Fact 4" "Polluted water can kill both baby salmon that are developing and the adult salmon that are on their way to spawn."
Epigenetic factors, such a water pollution, can affect the development of salmon, or indeed any fish; not just killing the developing fish, but also leading to malformations. This of particular importance when you consider the economic value of farmed species such as salmon.

Is it any good? It like a novelty record, and I suppose it is. However, the Chemical Brothers arn't about to release any old rubbish. It's novelty in the Lemon Jelly style, rather than the Mr Blobby one, and unlike Mr Blobby the guest rapper, Fatlip who used to be in the Pharcyde, is ace. Not to mention that salmon are a type of fish. Fish are still cool right?

HIM and The kiss of dawn

The HIM proteins , or "High Incidence of Males", are a group of 19 proteins found in the C. elegans. Interesting huh?

Is it any good? As much as I'm not into worm genetics, I'd rather would enjoy sitting though a 5 day conference on gene-protein interaction in C. elegans than waste another 3 minutes 55 seconds of my precious life listening to this again.

Monday, September 03, 2007

Science Singles, as seen on the famous internets

Here you go, have reviews of two of this weeks singles with a scientific meaning crowbarred in.

First it's the ever-lovely Magic Numbers with Undecided

Science? Bear with me here, it's going to get a bit nuclear physics. The nucleus of an atom is made up of two types of subatomic particle, protons and neutrons, known collectively as nucleons. According to the shell model of the nucleus, these particles are arranged according to energy levels in to "shells", much like the way we think about the arrangement of electrons orbiting the nucleus. When these shells are full, the nucleus is stable, and the number of nucleons needed to fill each shell is knows as a magic number (phew! we got there in the end). At the present time, science knows the following magic numbers: 2, 8, 20, 28, 50, 82 and 126. The band the Magic Numbers hail from west London, and are made up of two pairs of hippy brother and sisters . At the present time, science doesn't know if the Magic Numbers know anything about nuclear physics.

What does it sound like? It's oddly familiar. Like when you try on a new pair of jeans, and you instantly feel comfortable in them. It's only when you get home that you realise they are remarkably similar all you other jeans. It's one of those Magic Numbers songs: it has a fairly driven bit, a slower quite bit, an a cappella break bit, and a drum pick up bit back up the driven bit. Not original, but it works.

It's that Emma Pollock with Acid Test

Science? The term "acid test", meaning a decisive test, is used for all sorts of things these days. Back in the day it was only used to test if gold was gold. Due to it's complete outer shell of electrons, gold cannot easily give away or receive electrons, and as such it is inert. Put nitric acid on most metals and you will oxidise it, that is to say give away spare electrons. This results in the formation a metal nitrate salt, nitrogen dioxide and water. Since the salt is soluble, the treated metal will dissolve It will not, however, react with gold (or for that matter platinum, which is also inert).

What does it sound like? Meh, I never really was into the Delgados (she used to be their singer), and this leaves me unmoved. It's perfectly nice and everything, but it doesn't really have that something that other non-cutting edge people, such as the afore mentioned the Magic Numbers, have. In her favour, however, is the fact that she had a single called Adrenaline and the Delgados were signed to the Chemikal Underground label, both factoids being suitably almost sciencey for me. And pollocks are a type of fish. Fish are cool right?

Tuesday, August 28, 2007

Science Singles, what what.

I know this is late, but hey, it's been a bank holiday, and I've got a paper that needs writing.

This a top week for sciencey pop music. Behold:

Amylase by Cajun Dance Party

Science? This one is an absolute gift. Amylases are genuine enzymes (biological catalysts) with a genuinely important roles in physiology. No spurious links here, ho ho ho, no siree bob . The amylases (there are three different classes, alpha, beta and gamma) are enzymes that breakdown boring old starches into tasty, tasty glucose. You produce alpha amylase in your pancreas, to break down starches in your intestine, and in your saliva (see picture below) so you can start get the glucose form starch whilst you chew. Beta amylase is produced by plants, including ripening fruit, to break down their starches to sweet glucose. I'm not 100% sure what gamma amylase does. Something in the liver. Possibly to do with glycogen. Anybody?

Is is any good? La la la, jingle jangle, nice middle class boys and girls with messy hair, trendy jeans and guitars. So far so hip and down with the kids (gah, I'm getting old). "We need a catalyst" they sing. Ah, well, what catalyst would you like? Look, they are running through the country side. They must mean beta amylase, to ripen all that grain. "You're the catalyst that makes things faster, amylase will dry out the plaster". Huh? Amylase does what? How? Who? Where? Gah, I'm sure I'd know if this was balls if I'd just sat my GCSEs, as they have. Oh to be a teenager again. But not me when I was a teenager. Oh to be a popular, cool and attractive teenager.

Next are Múm and the improbably titles They Made Frogs Smoke Til The Exploded

Sceince? Obvioulsy Múm have been reading this research, "Adaptation of an amphibian mucociliary clearance model to evaluate early effects of tobacco smoke exposure" by Zyas et al, Respiratory Research 2004, 5:9, and then added they exploding bit to make it more exciting. Well done Múm for championing esoteric research articles that observe how bullfrog palates are affected by tobacco smoke.

Is is any good? Yes! Its like the happy dreams of a Texas Instruments Speak & Spell.

Friday, August 24, 2007

Big up the woo-busters. "out of body experience" induced

Woo! Woo! That's the sound of the police.
Woo! Woo! That's the sound of the beast.

Woo woo is also a rank cocktail.

"Woo woo" is also what ghosts say in the Beano.

Woo woo is also a on-line geek name for supernatural and irrational beliefs and explanations for stuff.

One such example of woo (as all the cool geeks say) is the out-of-body experience. This is when you can float above you body and see your self form above. All very spooky.
However, all over the papers like a rather annoying rash, is this story, where Henrik Ehrsson and his colleagues induced the phenomenon by the use of some sensory trickery.
But they didn't actually induce an OoBE (is that the acronym?), the patients' conciousness didn't actually fly above their bodies.
The brain is an odd thing. So odd, it's bonza.

Thursday, August 23, 2007

A better place than this

Do you ever read a a science blog, or may be a medical science one, and think:

"Hey! This is pretty much what I wanted to do when I started my rubbish science blog. But their attempt is much better than mine. Curse them, curse their eyes."

I do. Curse. Their. Eyes.

Monday, August 20, 2007

Science Singles, innit

Oh dear god no, first up is Linkin Park with Bleed It Out

How the hell are you going to tell me this is sciencey? Back in the day, before the advent of modern medicine, it seems that those trusted with the treatment of ailments seemed to be more interested in hurting their patients. One way they did this was by blood letting, which remained stupidly popular up until the 18th century, a long time after William Harvey had told everyone it was a bad idea. Obviously idiot kiddie metalers Linkin Bizkit (or whatever they are called) are joining the call for a return to pre-enlightenment medicine. Other songs off their forthcoming album include "Mustard Compress", "I'm Not Schizophrenic, I'm Just Possessed" and "Fuck Antiretrovirals, See a Faith Healer".

But is it any good? No. It is no good. It is bad.

Hurray! it's Aqualung with Pressure Suit

Science? Once again: hurray! Both the name and the title are sciencey. An aqua-lung is one of the original names for SCUBA diving equipment. Unlike earlier diving suits, aqua-lungs, developed partly by Jaques
Cousteau (with no little help from the engineer Emile Gagnan), were an open system. Air was passed from the tanks, to the diver, then released out into the water. This allowed for a lighter, more portable set or equipment, and led to modern sub-aqua exploration.
Pressure suits are are worn by pilots who fly at such altitudes that the air pressure if so low that to try and breath even pure oxygen they'd cark it. This includes astronauts' suit.

Is it good? Actually, it's a bit dull.

Tuesday, August 14, 2007

Brian May handed in his PhD

Look, this is quickly becoming Big Up Science and Pop Music. I apologise.

Brian May has handed in his PhD thesis, just a few years late (36). The press seem to be suggesting that he's got his doctorate already, but he still has to have his viva. Imagine being on his panel...

Monday, August 13, 2007

Science singles

I'm comin' up, so you'd better get this party started (gosh, I never noticed the blatant class-A meaning of that song before), here's this weeks almost sciencey tracks.

From Yesterday by 30 Seconds to Mars

Science? To get to Mars in 30 seconds would involve you travelling at least 1 900 000 000 metres per second, assuming you take a straight line when Mars it at its closest to Earth, which is around 57 million kilometres away. This, the black-hearted necromancers tell us, is impossible as it exceeds the speed of light (299 792 458 metres per second).
How does it sound? Gash.

How Do I Breath? by Mario

Science? "How", silver voiced Mario asks, "do I breath?" . Who'd have thought that behind that smooth RnB front, Mario is an inquiring soul crying out for knowledge about human physiology. Well Mario, contraction of the diaphragm pulls the abdomen downward, there by increasing the volume of the ribcage. The resulting negative pressure gradient pulls air into the lungs where it oxygenates the blood via the alveoli of the lungs. Relaxation of the diaphragm makes the thorax small, forcing the air back out the respiratory tract. So now you know Mario.
How does it sound? Virtually unlistenable.

Thursday, August 09, 2007

Foot and mouth

It's all going mad over at the Institute of Animal Health in Pirbright, Surrey.

First it seems that the latest outbreak of foot and mouth disease may have come from the IAH or a near by pharma lab, and now the IAH has an outbreak of legionnaire's disease. I suppose that's what you get when you work with scary bugs.

I went for an interview at the Pirbright labs a few years ago. It was the first time I'd been to such a secure lab. I turned up in a suit and tie which I had to take off and get into disposable overalls in order to visit the labs. On the way out I had to shower (but I think that was just because I'm a scummer).

Tuesday, August 07, 2007

Science singles

If there's one thing we love here at Big Up Science (and I say "we love", but I mean "I love", the Scientician's Accomplice has been oddly silent for some time. I'm worried, should I call the police?) it's science cropping up in "the arts" and "popular culture", whatever those words actually mean.

Starting this week we'll (I say "we'll"...) be compiling a list of any sciencey things, no matter how tenuous, in any newly released UK singles. What with the iTunes led death of the music single being heralded by all the trend watchers, I'm once again on the cutting edge of the Zeitgeist of UK popular culture music scene...

Here are the science singles for the week beginning 6/08/2007.

First up is Get Up by Elektrons.

Here comes the science bit: "Elektrons" is electrons, negitivly charged sub-atomic particles, but with a k where the c should be. Clever.
How does it sound?: Other than the band name, I'm not hearing any science, but I'll let it off by being a good tune. And it has Soup from Jurassic 5 on it. And a giant cartoon robot in the video.

The other sciencey release this week is Bench Sleeping by My Little Problem.

Here comes the science bit: "Bench Sleeping" is what you do when you've not got enough sleep before going into the lab. After setting up an experiment, you decide to flout all health and safety rules and get 40 winks at your bench.
How does it sound?: Disappointingly this is not the tale recalling events like those suggested above. It's quite nice though, but it's so gentle might make me fall asleep at the bench.


I wish I could write this.
Though they could have added more similarities: both have 7 cervical vertebrae etc...

(the second sentence explains the first I feel)

Tuesday, July 24, 2007

We are testing on more animals than we have for 15 years. I think this may be mostly my fault. I'm sorry. I'll stop it right now. There, i have now officially stopped.

Seriously, I have. That's nothing to do with the fact that I've just about finished my lab work. I've proved it by using this blatantly stolen picture of a lab mouse, rather than going to take a picture myself. Honest, it was exclusively for missplaced ethical reasons.

But wait, read on. Tests on primates are down 10%. Why isn't that the lead story? That's great news, but no one wants to hear that sort of news. Or maybe rather no one in the media wants to report that.

(please direct all death threats to someone else)

[Edit] typo promptly changed

Thursday, June 28, 2007

This sounds familiar

Once again we're ahead of the curve. LOOK!

I reckon they just read what we said about their publishers and decided to get their own back...

one all New Scientist... One all.

Monday, June 18, 2007

A ditty to the tune of the Superman Theme...

[In celebration of the first giant manta ray born in captivity at the Okinawa Churaumi Aquarium in Japan.]

Der de de de der
Der der der

Der de de de der

[this better be the animal of the week next week.]

Thursday, June 14, 2007

You know what I freakin' hate? I freakin' hate freakin' adverts for products with freakin' "good bacteria" in them, or even worse, freakin' "friendly bacteria". Awwww, look the cute little microbe? What's that Mr Lactobacillus casei immunitas [tm]? You think I'm looking nice today? Why thank you. What a friendly bacterium you are. Freakin' bull freakin' crap.
Any way, every thing friendly isn't always good: friendly fire for example.

Well, (in plataspid stinkbugs at least) these EVIL (yes, not friendly, EVIL!) bacteria are making their hosts eat soya. SOYA! Why I outta...

Friday, June 01, 2007

Reed-Elservier decide to stop being evil.

Wow, my faith in humanity is in a little way restored today; Reed-Elsevier have announced that they are going to stop running the DSEi and other arms fairs.

In a statement, they announced:
"it has become increasingly clear that growing numbers of important customers and authors have very real concerns about our involvement in the defence exhibitions business.

"We have listened closely to these concerns and this has led us to conclude that the defence shows are no longer compatible with Reed Elsevier's position as a leading publisher of scientific, medical, legal and business content."

Which appears to be a victory for those with any sense. Woot! I wish this sort of thing happened more often.

Tuesday, May 22, 2007

The end of the galaxy as we know it.

I've long suspected that physics is a dark art, evil magic if you will, and that physicists are blackhearted necromancers. Now I have proof.
Apparently they've known for decades that in a mere 2 billion years the Milky Way, the galaxy that we call home, will collide with the Andromeda spiral galaxy and they never tell anyone about it, nor do they seem to doing anything to prevent this cataclysmic event. The gets.

Now they've used their demonic ways to calculate that during the event our humble solar system will be cast out of the party zones of the galaxy, and dumped unceremoniously in the outer reaches of the new one [1].
Apparently, the consequence of this is that we are royally fucked as a planet. And I don't even know if that new planet what they found will be ok. It's almost enough to put you off you tea...

The Collision Between The Milky Way And Andromeda.
T.J. Cox, Abraham Loeb . May 2007. e-Print: arXiv:0705.1170 [astro-ph]

Monday, May 14, 2007

How a beetle made an idiot of a hamster

Richard Hammond, aka, "The Hamster", is an idiot. This, I feel, in not really news, but I figure it needs reiterating, especially as he's just written a column in the Mirror stating how may-bugs (cockchafers) are proof that evolution is bollocks.

His main point seems to be that may-bugs are rubbish, and the spend all their time flying into houses that they must never get chance to reproduce. How does he think they do reproduce? Spontaneous generation?

He has taken the intellectually easy option of discounting evolution based on limited personal observations. He's obviously got thinking about it, and rather than perusing the thought through, and finding out about cockchafer life cycles and how they may work in the ecological niche to which they've adapted, he's made made assumptions based on a poor understanding of darwinian thought, an afternoon in the garden and five minutes on Wikipedia. Knob.

EDIT: Title spelling changed. Originally spelt Beatle, as in the pop combo.

Friday, May 04, 2007

Protein Synthesis! Hippies! Dancing!

This might be one of my favourite things ever.

Although some of the words, including the final line "all mimsy was mRNA, and Protein chain outgrabe" just before the wigout at the end, do leave me somewhat confused. But I think that's becuase I'm a straight, not a wild crazy hep cat.

Tuesday, May 01, 2007

I heart Seed Magazine: Byrne and Levitin

How great is Seed Magazine?
The answer is 12. 12 great.

Great "Seed Session", with David Byrne (a musical genius, up there with Stevie in the hero rankings) and Prof. Daniel Levitin (used to be a session musician and sound engineer, but now is James McGill professor of behavioral neuroscience and music at McGill University) having a good old natter about the neuroscience of music and all dat wicked shit man...

DB: So when you watch a performance, sports for example, you're not only watching somebody else do it. In a neurological kind of way, you're experiencing it.

DL:Yeah, exactly. And when you see a musician, especially if you're a musician yourself--

DB: —air guitar.

DL: Air guitar, right! And you can't turn it off—it's without your conscious awareness. So mirror neurons seem to have played a very important role in the evolution of the species because we can learn by watching, rather than having to actually figure it out step-by-step.

Friday, April 27, 2007

microRNAs are really, really important.

The first mouse knockouts for a microRNA (miRNA, short interfering RNA or siRNA [1]), has revealed that it has a important role in the immune system and for homeostasis.

In the work, by people at Cambridge University's Babraham and Sanger Institutes and published recently in Science [2], they knockout out bic/microRNA-155, and got immunodeficient mice that also had funky airways due to them (the airways) being remodelled more.

siRNAs are a fairly recent discovery, and we are only just getting our heads around that fact that they have an incredibly important role in how the genome is used by our cells.
The fact that such regulatory effects can have such a massive effect on the immune system and homoeostasis is really some thing.

All this makes me wonder if any of my own work, which looks at the roles of signalling molecules in the developing skeleton, means anything without knowledge of what siRNAs are doing. That's depressing.

[1] a small, single stranded sequence of RNA which, instead of coding to make a protein, acts to regulate expression of other genes.
[2] DOI: 10.1126/science.1139253

Friday, April 13, 2007

Can a crocodile bite a man's arm clean off?

You've no doubt seen the story of the man who's arm was bitten off by a crocodile in Tiawan.
The arm belongs to vet Chang Po-yu at the Shousham zoo in Koahsiung.
It's a strinking photo isn't it?

The thing is, are croc's teeth not adapted for clamping, not cutting? Don't they bite their prey and drag them whole into the water to drown, rather than tear chunks off?

The teeth of most crocodillians are fairly short, uniform and cone like, perfect for clamping down hard on to a tasy vet's arm, but not cutting it clean off. They don't occlude in such a way to allow shearing and cutting of meat, like your front incisors do.

So what happend here? The arm looks severed just over half way down the forearm. You'll notice the the Did the crock clamp down, crushing the bone and then the skin and muscle tore off? Did the arm get clamped in, and the paramedics (or whoever) cut him free, leaving his fore arm in place? Or is the photo a fake?

Wednesday, April 11, 2007

Science Mix Tape = SciPop

In a beautiful example of the convergence of memes, the people over at Null Hypothesis have been making a list of science rock and roll songs. Well done them, they have a much bigger list than ours.

Perhaps it is due to their brighter minds, keener understanding of the zeitgeist and larger music collection? Or maybe it's just that more than two people read their site (that's right, our readership is growing)?

I must say though, I see Atomic Kitten listed for "The tide is high". That's not cool. That's not cool at all. It's the Paragons, or I'd also accept Blondie, but Atomic Kitten? Words fail me.

Dropping Science 2

A selection of suggestions for the mix tape from Blue and Brown and Dan, up form the comments.
Firstly, blue and brown's, note that there is a ban on all coldplay:

Apologies to Insect Life - British Sea Power.
The Test - The Chemical Brothers
Nature Boy - Nick Cave and the Bad Seeds

Now Dan's
Bovine Spungiform Economics - Million Dead
Biological - Air
Gene By Gene - Blur
Tendon #7 - Chris TT [late addition due to non-emo nature, that and the fact that he lists Dawkins, Darwin, the Nat. Hist. and Sherlock's bro as influences on his MySpace thingymajigger, good man.]

(I'm going to ignore the rest of Dan's as they are either too emo, or I havn't heard of them... Or both)

Tuesday, April 10, 2007

dropping science

More suggestions for the science mix tape:

"Inertia Creeps", Massive Attack
"Particle Man", They Might Be Giants
"Mercy Mercy Me (the Ecology)", Marvin Gaye
"Girl, You Have No Faith In Medicine", White Stripes

Big dog, little dog, single gene, dwarf mice and many authors.

Research published in Science shows that variation in a single gene, insulin-like growth factor 1 (IGF1), may determine the body size of domestic dogs [1]. IGF1 is one of those growth factors that crops up all the time in skeletal development (mouse knockouts, for example, exhibit achondroplasia [2]), so it's not a shock to see it here. Though it is pretty cool science. You can read all about the ins and outs of this in other places, I've got another point to make.

There are 12 people on this paper. 12, from 8 different institutions. This is fairly typical for Science, Nature, Cell papers, and indeed any other high impact paper. People get put on papers to add weight to the research, or to embiggen friends, bosses and spouses. I have heard of at least one researcher who puts their partner on to papers, even when the partner in question has had nothing to do with the actual research, and conversely I know of students and technicians who have put the hours in to actually do the research for a paper, only to be thanked by being left off the paper, sometimes not even making the acknowledgments. These practices, whist being widespread, are dodgy at best and down right fraudulent at worst.

As I've said before, I'm just a lowly PhD student, and who am I to comment, but the whole situation leaves me saddened. Though, that said, if i was to be put on to a Science paper with out lifting a finger, would I get on my high horse and ride out into moral sunset? I doubt it.

I've copied the International Committee of Medical Journal Editors' guidelines on authorship below [3]. I'd be very surprised if all 12 authors on this paper fulfil all three criteria of the first point below, though I'd love to be wrong.

    • Authorship credit should be based on 1) substantial contributions to conception and design, or acquisition of data, or analysis and interpretation of data; 2) drafting the article or revising it critically for important intellectual content; and 3) final approval of the version to be published. Authors should meet conditions 1, 2, and 3.

    • When a large, multi-center group has conducted the work, the group should identify the individuals who accept direct responsibility for the manuscript (3). These individuals should fully meet the criteria for authorship defined above and editors will ask these individuals to complete journal-specific author and conflict of interest disclosure forms. When submitting a group author manuscript, the corresponding author should clearly indicate the preferred citation and should clearly identify all individual authors as well as the group name. Journals will generally list other members of the group in the acknowledgements. The National Library of Medicine indexes the group name and the names of individuals the group has identified as being directly responsible for the manuscript.

    • Acquisition of funding, collection of data, or general supervision of the research group, alone, does not justify authorship.

    • All persons designated as authors should qualify for authorship, and all those who qualify should be listed.

    • Each author should have participated sufficiently in the work to take public responsibility for appropriate portions of the content.

[1]Sutter et al, 2007, DOI: 10.1126/science.1137045
[2]Wang et al, 2006, DOI:10.1210/en.2006-0196
[3] accessed 10/04/2007

Friday, March 23, 2007

Rock and roll science

I'm getting used to this slightly higher frequency posting game. It won't last.

Anyway, in my last post I mused if any (succesful) rock musicians quit the road and hit the lab. But I'd also be interested to hear of any link between rock and roll, and the world of science. So far, other than Dr Bryan May, all i can think of is that guy from the Offspring starting his PhD at UCLA, or the University of Southern California, or some place, but never finished it. Oh, and doesn't the guy from Bad Religion actual have a PhD?
Are there any good rock star scientists out there (other than Bryan May, the man is a legend), or are we stuck with rubbish Californian punk bands? I'll have a think and report back.

I'm also wanting to put together a mix tape of Sciencey tunes; here are a couple to be starting off with.

"Go Tell The Women", Grinderman.
"Lesson 6: The Lecture", Jurrasic 5
"The Scene is Dead", We Are Scientists
"Dr Funkenstein", Parliament

watch this space....

Thursday, March 22, 2007

Heavy Metal Teen Geeks

New Scientist's (boo Reed-Elsevier, boo!) blog rightly points out that research suggesting heavy metal music is listened to by clever kids is a bag of wank (I paraphrase). Actually, the research says they listen to it to cope with the stress of being gifted. Told you, a bag of wank.
The best thing is, if you click back to the Telegraph (I mean, come on, the Telegraph for feck's sake!) article linked in the blog post, you get a picture of Bryan May getting his (honorary) doctorate. Bryan May! How good is that?

Oh my, this is the third post in a week. I feel light headed....

EDIT: I feel a bit bad about this. I did some more digging, and the research was done by one Stuart Cadwallader at Warwick and the NAGTY. He's doing an only MA in psychology, and I assume this is part of his MA dissertation. I'm glad my MSc (yes, MSc, I'm still going to be a twat about this not being science, Ha!) never made the national press, cos ill informed bloggers would tear the bejesus out of that rubbish.
Shit, it seems part of his masters level research is being presented to the British Psychological Society, so really that's mightily impressive. No offence Stuart.

I'm sure NAGTY is a super institution, and the research is top notch. I think I am mostly enraged by the telegraph article. And Bryan May. He left his PhD for rock and roll, can anyone think of someone doing the reverse? A professional popular musician quitting to work in science?

EDIT 2: No, this is a bag of wank. Still, no offence Stuart. It's not your fault that you MA project made it onto the national press.

Tuesday, March 20, 2007

The invasion of the GM mosquitoes

It's being reported in the Guardian and the Times (though the Times article seems better informed. Imagine that.) that the plan to release genetically modify mosquitoes, which are made to be unable to pass on malaria, is getting closer.

Traditionally, transgenic mosquitoes have been out competed by their wild type chums [1], but the big thing about this latest study, which is to be published in PNAS (but doesn't appear to be released at the time of writing), is that these mossies show in increased fittness, compared with the wild type.

Incidentally, reading the Times and Guardian articles, one gets confused as to who led the research. Is it Mauro Marrelli as the Times says, or, as the Gurniad has it, his colleague at Johns-Hopkins, Marcelo Jacobs-Lorena? I'm too lazy to go find out. That's the job of a journalist.

I suppose that I should say some thing about the controversy of releasing GM animals in to the wild, but you know, I don't think it's a worth while debate. Malaria kills more than a million people a year, most of whom are kids. Won't somebody please think of the children?

You know, just writing this gives me the willies. I have serious issues with mosquitoes. Nasty little fuckers. Almost as bad as daddy long legses. Now there is an evil insect. You know they suck the brains out of babies heads? It's true I tells ya .

[1]Trends Parasitology, 2006. 22(5):197-202 doi:10.1016/

Saturday, March 17, 2007

pretty pictures of a cell

This is a electron tomography generated image of a yeast cell. Nice isn't it?

Researchers at EMBL and the University of Colorado have published this in Developmental Cell, as part of their research into the cytoskeleton.

The image was made by taking electron micrographs through the cell (transmission EM I assume, I'm at home and don't have access to the journal to check. This is blogging by press release, but then I'm feeling lazy), and then making a 3d reconstruction using the stack of images, much as you would when doing CT scans of people. Well, not how you would, unless of course you are a radiographer. Do I mean radiographer, or radiologist? Or both?

Monday, February 26, 2007

Elsevier promote arms sales

Really, this update, which the first in a very long time, should be pithy, "comical" and light hearted. Especially as our one reader has viciously slandered me on their site.

Alas, it isn't to be.

Thanks Dr Ben Goldacre's Bad Science column in the Guardian, (and associated blog) I recently discovered that Reed Elsevier are involved in running trade fairs for arms manufacturers.

Remember kids, guns and bombs, death and destruction, all that stuff is bad. The arms industry is bad. It doesn't take a genius moral philosopher to work out why.

I'm writing a paper at the moment. You try and write a paper about biology and not think about publishing it in an academic journal owned by Elsevier, they publish the vast majority of all reputable journals in the biological and health science, including some of the biggies, such as the Lancet. Richard Smith[1] has recently published an engaging editorial on this very matter in the Journal of the Royal Society of Medicine pointing out the irony of health journals beng published by the agents of death[2], especially as the Lancet has published a few high profile pentagon baiting articles on the civilian death toll in Iraq and the danger of cluster bombs. I've no idea what it's like in other fields, but I wouldn't be surprised to find Elsevier dominating there too.

What to do? Well, protesting, boycotting and petitioning are all great places to start. It's easy to sign the petitions and wave a placard, but is what about boycotting? I'm finding a conflict between my ethics and my desire to get my first publication into the most respected and widely read publications possible. It's shite, especially as KCL (where I'm based) is not a full member of the open access published Biomed Central, and so to publish in their (equally excellent) journal will cost my grant several hundreds of pounds.
In my case, unless my boss and collaborators pull rank, morality will win out. and I'll ask to publish somewhere else, probably to the detriment of my CV. But I'm just one little [3] PhD student working in a rather obscure branch of biology, what difference will I make? It's time to get organised. As Richard Smith wrote:
It is essential, however, to act together. Somebody
needs to orchestrate a campaign. The people in the
strongest position to do so are the authors and readers of
The Lancet and the 2000 other journals. Who will take the
I'll get off the soapbox now. Occasional, poorly written things about science will continue to be posted in the future.

[1] medical doctor, former editor of the BMJ, journalologist (is that even a word?), and brother of comic Arthur Smith, that, as they say, is a fact!
[2] excuse the melodrama for a moment please
[3] ok, ok, I'm not little, but I am inconsequential.