Friday, 21 November 2014

Human universe - are we alone?

I have to admit I was really disappointed with the second episode of Brian Cox's latest trip around the world documentary series but I was glad I gave it another chance. I'm a sucker for anything about the possibility of alien life and this 1 hour documentary summed up the possibility for life out there.
Some spoilers to follow.

 In one sense the numbers are stacked in life's favour with there being billions of potential stars and current data suggesting there are billions of planets that could sustain life. Cox does a good job of explaining why the odds vastly reduce when you consider the possibly unique event of the symbiosis that created eukaryotic life on our planet. He then reduces the odds further by introducing the Fermi paradox which states any intelligent life existing 10 million years prior to us would have fully colonised the galaxy. I guess they could be more adherent to the laws of Star Trek in not interfering or civilizations burn out before they can escape their gravity well.

The show ended well with the sobering thought that if we are the only intelligent beings* out there ** then we have a responsibility to protect this unique situation and to go out there and explore. I particularly like the latter idea (it should also help with preserving other life on earth) of us going out there and colonising (preferably empty planets as opposed to conquering others). I'm a firm believer of humanity having to create its own aliens - give us a few millenia on different planets separated by near impossible distances and we'll eventually evolve into our own Klingons and Ewoks.

Anyway - a solid episode that has me willing to give the remaining episodes a chance.

*Don't worry he acknowledges there's plenty of intelligence on our own planet - something I think we really need to acknowledge. His point was that none of these animals are physically capable of building things (with the exception of primates and possibly the octopus with some minor mutations) that would allow them to communicate beyond the stars.

** He sticks to the Milky way for what I assume is the fact that a) all bets are off when you include the universe (as you multiply the chance by at least 100 billion) and b) the distances between galaxies are vast even if you happened to be next door to an intelligent galaxy.

Wednesday, 19 November 2014

Biology on TV

Bit of a personal slam from a quote on "the Blacklist"

"anyone working with Cullen is doing so in isolation, illegally and for no good purpose"

As an aside, the show is fun but rarely has much biology in it. If anything it has the most glaring example of "why don't you perform a DNA test?" I can think of. It's like the show exists in a world where paternity testing doesn't exist.
Otherwise the biology is usually in the hands of people who could make billions using their amazing findings legitimately but decide to use them for "EEEVILL" instead. Case in point, the episode I quoted from where a biologist who came up with a cure for a disease decided to use it to blackmail people with as opposed to selling said cure. It would have been a dull episode though,
Another curious example of science was in an episode where [mild spoilers for an episode that aired a year ago] a scientist deliberately infects large groups of people with a disease (which he magically turned into a virally bourne version of a genetic disease) in order to find a person with natural immunity whom he could then study and find a cure. I'd like to see the reaction of the review panel looking at that grant outline!

Thursday, 16 October 2014

Your life on Earth

I found this cool feature on the BBC today. Plug in your date of birth and height and you'll get a ton of interesting facts from how much a redwood has grown to how far you've travelled through the Galaxy during your life. There's also some interesting/scary statistics regarding population (which ticks up as you read) and use of resources that really made me think - as well as selfishly worry that it's something that could easily be an issue in my lifetime.
Anyway, I won't spoil it all and let you discover the nuggets of information for yourself.

Thursday, 9 October 2014

Personality test for Biologists!

Cell Signalling Technology recently came up with a crafty form of targeted social media advertising in the form of "what kind of protein are you?" If my workplace is anything to go by it has prove quite successful.

I got "Chaperone" - "You are a nurturer, your calm and efficient manner brings organization to an otherwise chaotic situation. People look to you for help with projects and advice."

I think many would differ on that description!

I noticed there weren't that many outcomes so I think the following could be included.

p53 - it's all about you, you're the centre of the universe and love all the attention people give you although deep down you know you don't quite live up to it.

Protease - You have a profound effect on everyone you meet - for better or worse. You can release people's true potential or destroy them.

Prion - you hang around in the background feeling like no-one notices you. You'll get the last laugh though as you slowly work you way up to the top, causing others to bend to your will.

Haemoglobin - you are the life of the party, a breath of fresh air. A good motivator of others and able to take a lot of crap off people.

I'm sure there are others feel free to suggest some!

Wednesday, 8 October 2014

BBC Horizon - Is your brain male or female?

It's one of the classic nature vs nurture questions -  are men and women different due to societal pressures or are there genetic/hormonal factors that allow differences to be observed? The documentary does a good job of presenting evidence from both sides and rather than give us an answer leaves us to judge. The fact the show can't decide whether there's such a thing as a male or female brain renders the title question a bit moot. So you'll be disappointed if you are hoping to get an answer to that. The rest of the show is very interesting though and the parts that stood out for me were;

Showing that monkeys have a gender bias to toys that is the same as in humans. Not sure monkey parents could introduce that bias (although not completely impossible).

Showing that research suggests a correlation between testosterone levels in the womb and the severity of autism. It was also interesting that autism could be seen as extreme "male" behaviour. Women are also exposed to testosterone so can still be autistic but this result also fits the observation that autism is more common in males.

That some of the observed differences in spatial awareness disappear when tested in a way that the subject doesn't see it as a spatial awareness test. This raises two important issues - the tests may have a bias towards a gender and that being told "women can't do X and men can't do Y" can be a self fulfilling prophecy.

That medical treatments may become gender specific. I suspect this one may be skipped over by personalised medicine which is already on the horizon. I guess gender specific medicine could still be a useful stepping stone though.

The one aspect of the show I didn't really enjoy was the male and female presenter format, I can see why there was the temptation to go for that angle but it felt a bit forced having them fall on different sides of the fence. Was that supposed to be a male vs female bias? I also felt one of the presenters was cherry picking the evidence eg refused to accept genetic components for things the other gender is apparently better at but apparently being ok with it when it was their own gender with an advantage. Or maybe that's my gender bias? My sample number of 2 suggests it wasn't.

Usually the answer with these polar explanations is the obvious "a bit of both" and I definitely think that's the case here. With regards to nature we'd be foolish to think the X and Y chromosomes are solely responsible for behaviour, For example if having a Y chromosome is " - 5" for having empathy, there's probably at least "+ 10" for empathy floating around on the other 22  chromosome pairs. this would explain the variety within a gender as well as the fact there are crossovers. Just as personalised medicine will supercede gender-specific medicine, so too will the genome overcome the X and Y chromosomes with regard to behaviour.
In terms of nature; I do think society needs to make a concerted effort to iron out gender stereotypes as the evidence presented in this episode shows how it can make the brain behave accordingly. Far better to convince both genders that they can be ambitious, capable in any discipline and have the full range of emotions than to put either one at a needless disadvantage.

Saturday, 27 September 2014

BBC4's "the wonder of Animals"

Chris Packham is back with another science-skewed focus on natural history with his new show "the wonder of animals". Each episode focuses on a species of animal and then looks at the science of how it has become so successful.
The first episode was about Penguins and how their feathers are masters of insulation but can also be used to aid acceleration under water via the release of air bubbles. Another episode claims Foxes can sense magnetic fields for hunting and the science behind bear hibernation is truly fascinating. All of these things have me thinking "how can we use this technology for ourselves?". The muscle-wasting defence in hibernation sounds very useful for incapacitated patients and astronauts. for example.

I think there's still a few episodes left but for those with access to BBC iplayer and like their shows in 30 minute chunks, "the wonder of animals" is well worth a look. Just don't think too much about how this knowledge was obtained - the show neatly avoids that.

Here's a taster

Tuesday, 26 August 2014

Science Songs

Since getting back from holiday I've been having a nightmare getting a certain type of PCR to work. The most recent head scratching moment was to get a round of PCR that worked perfectly. I immediately ran the same PCR with the same reagents and settings but with the DNA samples I wanted to check. Nothing worked - not even the positive controls that had worked 3 hours earlier.
When an experiment can't be repeated with the same conditions there's only a few explanations;
a) there's something you aren't accounting for so it isn't the "same"
b) you are the variable
c) you are switching universes in between experiments
d) there are science goblins messing with your mind

All of these options reminded me of this song

The chorus is

"There are monsters here
And as you scream it makes no sense
It makes no sense
It makes no sense at all "

That pretty much sums up the last 2 weeks of work for me.

Saturday, 12 July 2014

Science Meme/Quote

Straight and to-the-point and worth picturing whenever some non-sensical "science" article turns up online. Good old Carl Sagan.

Monday, 7 July 2014


Here's a link to a promo for the "happigenetics" project. Can't say I have a clue what it's about but it seems curious never-the-less. There's some more info here for those who are curious though.

Besides the great name and the fact I know some of the people involved, I think it's great that scientists are trying to show off their creative sides. To a scientist it's pretty obvious we're creative or we'd never come up with new techniques, find ways around problems or save money/time on experiments. I can see how the rest of the world may think scientists are the antithesis of creativity with regards to artistic endeavours. As this clip shows, that's really not the case and creativity can be applied to various things be it science or art. I'm sure there're a lot of artists out there who could probably come up with some great experiments too.

Tuesday, 24 June 2014

Whole Lotta Love

One of the great things about Science is, no matter how much time you spend working on something, there is always some super cool fact that takes you by surprise.
In this instance I discovered something about flies that I was completely unaware of until I went to a Fly seminar. Flies have 3 hearts - the main heart and an additional small heart for each wing. That's ONE more than a time-lord!
I was hoping I could find a video of them beating but have failed. I'll try and ask the person who gave the talk if I can borrow the clip.

I guess this is true of many winged insects. Which makes me wonder if a dragonfly has 5 hearts?

Sunday, 22 June 2014

Office science

This offensive item is currently living in an office that is acting as a temporary kitchen. It seems to be at the stage where no one will risk touching it for fear of an explosion.
The question is how long will the plastic stand up to the pressure? I guess only time will smell ...

Sunday, 8 June 2014

Forget Me Not

At around 9:30 pm last night I was about to make some food, open a beer and watch a film, when I suddenly thought "did I take those mini-preps out of the centrifuge after the final spin?". Surely I had, but the doubt lingered and I knew if I didn't nip it in the bud it would ruin the evening and probably culminate in a night where nightmares about DNA visibly decaying in front of my eyes would ruin my sleep. So I went into work. Luckily, it only takes 10 minutes if I jog.
Unsurprisingly, said mini-preps were comfortably nestled inside the freezer. The centrifuge lid was open in what appeared to be a mocking laugh. I walked back home and got a take-away so the trip wasn't a complete waste and nightmares about work were avoided.

Doubt is a dangerous thing.

Friday, 6 June 2014

Science Songs

 One transformant from my test plate and twelve from my negative control. I'll miniprep it anyway.

Listening to the lyrics of verse 1 and chorus more carefully, I 'm thinking this song should be a science anthem!

Thursday, 5 June 2014

Pint of Science Bristol 2014 summary

The pint of science festival happened a couple of weeks ago. More than 200 talks over 3 nights in 6 countries. The themes covered life sciences, neuroscience, chemistry, physics and Earth sciences. I'll admit that the most frustrating thing about being an organiser was not being able to see some of the other talks. Life Sciences was excellent (if i say so myself) but I was particularly drawn to some of the non-biology topics mainly because I know a lot less about them. One of the talks was on "morphing materials for cars and planes" which sounded a bit like transformers cool.

As I was at the life Sciences event I thought I'd do a quick overview of the three days.

Tuesday, 27 May 2014

Movie Science : X-men days of future past

I'm sure I've mentioned it before but the X-men cartoon and comics of the 90s probably bare a lot of the blame for me being a biologist. As such I still have a soft spot for them and was very impressed when I came out of the cinema having watched the latest instalment "Days of Future Past". Yes. I'm a big fan of the original comic storyline as well.

In terms of the science, I just have to accept that "mutant" is a license to do whatever you want, biology and physics be damned and I'm not complaining when it looks so cool. What I did find curious though was a bit of genetics in the film in which a character said they could detect people who could have mutant children or have grandchildren that could be mutants. This got me thinking, the films and comics often refer to a gene called the "x-gene" which seems to be the super awesome gene that results in all the mutant powers. I'm guessing it must be a transcription factor. The fact humans can have mutant children means the mutation is either spontaneous (a random mutation in the parent's germ line) or recessive (the mutant has to have two x-genes to be a mutant). But the grandchildren thing strikes me as odd because if it is recessive then you wouldn't necessarily have to wait an extra generation to get the mutant child. Unless two separate recessive mutant genes are required eg "x-gene" and "Z-gene". This might help explain why the mutants are so rare as well as the major variety in powers (maybe the other Z-gene encodes an epigenetic remodelling factor?).
That or the screenwriters didn't really consider the genetic implications of that sentence. In true Marvel tradition I'm providing a "no-prize" in case they need let off the hook.

If the genetics didn't make any sense on first read, hopefully this diagrams will help. Be warned it gets far too geeky from here on out.

Saturday, 10 May 2014

Mutant Fail

This song pretty much sums up the discovery I made on Friday.

Basically the Drosophila mutant I have (and have been performing various experiments with) is still being expressed, Which isn't great news when you've been assuming it is a null mutant (a mutation with no expression of functional protein).
The mutant is missing the first two exons and has lost it's original start (ATG) site but annoyingly it has chosen to pick up an alternate start site. This gets more tricky as there are two that are close together


If it has picked the first one then I should still be ok as it is out of frame has 8 nonsense amino acids and then hits a STOP codon. The problem is that the second one is in frame and would happily make the remainder of the protein that contains at least one domain that is vital to its function.
The unfortunate thing is that I have no way of telling which start site is being used without an antibody (which I don't have). If anyone knows of a way to do so - I'm all ears. The best I can come up with is to clone the mutant cDNA into a GFP vector and see what is expressed. Not a great experiment as the only thing it can confirm is whether a truncated protein is being produced,

Ultimately I need to make a genuine null mutant which is what my priority has to be. Somewhat worrying with 11 months left on my contract but I may as well get on with it.

In an attempt to see a positive in this revelation - it may at least explain the lack of a phenotype in the mutant I have been using. Maybe the real deal will have a phenotype that rewards the mutant making!

Monday, 28 April 2014

Egg on my face

In the lab today I asked whether there were any really old culture plates in the incubator as this often happens when one of the lab is away for a while.
One of my colleagues replied "No, but there's a bacterial plate with your name on it that looks over a week old in the other incubator".

Serves me right.

Sunday, 27 April 2014

Pint of Science - International

I mentioned a while ago that I'm involved in the Pint of Scientist festival this year. Handling the "Life sciences" section in Bristol (book your tickets now).
I know I have readers from other parts of the world and the website now has sections for USA, France, Australia and Switzerland. So if you live in any of those countries have a click and see what may be on in your area.

I'll try and do some more shameless promotion for the talks I'm involved in although I should probably concentrate on making sure they run smoothly first!

Name the Biologist

It's been a little while but here's a new "name the biologist". It's still techniques oriented, until it turns into something else, so the list of candidates should be shrinking

As for the last instalment that was none other than Paul Erhlich another Nobel Prize winner who among many other contributions popularised the "magic bullet" theory in which the magic bullet was a compound carrying a toxin that would selectively target and kill a disease-causing organism. This is partly seen in monoclonal antibodies. Erhlich also developed staining techniques for identifying different blood cell types leading to the characterisation of several blood diseases. He was also a pioneer in chemotherapy. A pretty spectacular career.

Saturday, 26 April 2014

Rick and Morty - Inspirational Science Motivation Speech

Rick and Morty is an excellent new animated sci-fi comedy from the creator of "community". Think of it as this generations' "futurama" but possible even darker. Anyway the show is littered with funny quotes but I quite like this one as a reason for studying science.

Also wise words for any scientists suffering in a relationship :)

Break the cycle, rise up and focus on science!

Monday, 7 April 2014

Colour Co-Ordinated

Only realised half-way through the day that the purple in my black and purple striped shirt matches my gloves and tube rack. I don't even like purple that much so it's a weird co-incidence.
That said it shouldn't be noticeable as I "always" have a lab coat on when wearing gloves.

In other news - don't flame coverslips in 70% ethanol and accept that cloning never wants to work when you think it should be a slam dunk done-in-one. At this rate it's not going to be a done-in-a-dozen.

Tuesday, 1 April 2014

Name the Biologist

This guy was responsible for quite a few interesting discoveries and concepts. It's hard to dodge his influence.

With regards to the last installment they were

Saturday, 22 March 2014

Name the Biologist

More technique based ones. This one is a little tricky but I'm going for the one who developed the most recognisable technique and the one who named it/helped make it popular. Plenty of clues before the picture this time!

Disclaimer: I can't 100% verify the person in the 2nd picture is the one I mean - but others online seem to have made the claim...

As for last week that was

Friday, 14 March 2014

Kiss My Ass(pirator)!

Friday afternoon lab fail. The aspirator jar was being cleaned out and rendering one of the tissue hoods unusable. I thought I'd be proactive, clean out the jar and connect it back up to the aspirator. All seemed well despite some confusion over the double jar system. Got a plate of cells out and went to remove the media only for the damn thing to turn into a mass of bubbles.  Culture ruined!

I guess I could have tried to work out how to get it to suck but when this kind of thing happens at this time on a Friday, the best option is to say "F@%k it" and avoid any further disasters. I did at least take the aspirator apart so others wouldn't be victim to it's anti-aspirating behaviour.

Wednesday, 12 March 2014

Pint of Science Festival 19-21 May 2014

A quick plug for this year's "pint of science" festival which will occur at several cities across the UK from the 19th-21st May. Not all is lost for those outside the UK as the event is also occurring in parts of the world (have a look to see if your hometown is involved).

The idea, as far as I'm interpreting it, is to engage the general public (who are allowed to drink) in the relaxed environment of the pub. Hopefully seeing scientists with a pint in their hand will make them (us) seem more human and approachable. Top researchers from the cities in question will entertain and educate ("entucate"?) you with their research and from what I've heard there will be anything from games to comedians in between the talks.

Biology is well represented this year with a "life sciences" and "neuroscience" themed subcategories along with "physical sciences" and "geological sciences" (if biology isn't your bag).

Why the plug? Besides it being a cool event in it's own right, there's also the fact I'm helping organise the Bristol Life Sciences event. Nothing wrong with a little self-promotion, right?

I'll keep you updated where possible and hopefully some of you will turn up to one of the events in your area.

Tuesday, 11 March 2014

Research Reality Check

The undergrad student who is currently working with got an unpleasant insight into the harsh reality of research today. After slaving away transfecting and staining cells for a week, we had a look at the results on a microscope and within the space of 3 hours destroyed what should have been 9+ hours of glorious picture taking. Perhaps even more importantly was the fact there wasn't any good reason for why they had all failed seeming that some of them had worked previously. I think it may be that the cells were a bit off. So tomorrow we will try with new, improved cells.
Today's results may not seem useful but it will be vital if the student ever considers a life in research.

Name the Biologist

Another week and another mystery biologist. In keeping with my current theme, this is related to a technique or tool that is invaluable to the regular biologist (although this one depends very much on your field and is becoming replaced by other techniques).

As for last week, it was Hermann J Muller - one of the pioneers of Drosophila research and the mutagenic effects of radiation.  The main reason I covered him though was for discovering balancer chromosomes - chromosomes with multiple inversions that are incapable of recombining with their sister chromosome. As someone who has worked with flies for a decade you have no idea how much easier this set of tools has made my life (and that includes you TM2 with your Ultrabirothax phenotype!)

Tuesday, 4 March 2014

30,000 year old Giant Virus - no longer on ice !!!

The BBC reported on a Proceedings of the National Academy of Science  about a "30,000 year old virus that has come back to life".  The interesting thing is that a virus can be frozen for such a long time and still function but it was clear the BBC wanted to make it sound like a horror film and I'm pretty sure that's what got so many people clicking on the story today. The researchers also seem glad to add fuel to the BBC's apocalyptic scenario of ancient/presumed eradicated viruses being unleashed due to global warming/mining.

The scenario of a giant killer virus from our ancient past does remind me of "the Thing" and several episodes of "the X-files" maybe now would be a good time for a topical horror film about giant viruses?
If I was a Hollywood screenwriter, I'd be writing the script for 2016's B-movie extravaganza. "it came from within the glacier" or "megasupervirus attacks". Here's some posters to help inspire them.

Or a new spin on John Carpenter's "the thing"?

Unfortunately the giant virus only infects amoebas and not human cells (phew) but they do point out that something like small pox could be frozen out there. It's always good to have another reason to be afraid of climate change.
Maybe the ice-age is the only reason mankind has made it this far and somewhere at one of the poles our nemesis is waiting...

Sunday, 2 March 2014

Credit it where it's due - The following

Mild spoilers ahead if you haven't seen episode one of "the following" season 2. The show is pretty dumb/bad but is a guilty pleasure of mine. It does get bonus points for acknowledging that identical twins have non-identical fingerprints though - something that Orphan Black, a show about clones failed to do.
Just thought I'd mention it rather than always bag on the ones getting it wrong.

Saturday, 1 March 2014

Control Freak - how did I get that hangover?

Recently I had an unpleasant allergic reaction to beer. Not in the "I had too much of it" way but more in the "it caused severe congestion, sinus blocking and even swollen eye-lids (not the result of a fight outside the pub)" way. It's not necessarily the alcohol and can be anything from histamines to wheat to some random ingredient in a beer that my body dislikes.

Friday, 28 February 2014

Name the Biologist

There's a clue in the picture besides the person himself!

I'll do the answer to the last installment over the weekend but if you're desperate I can provide the name now. It was Koichi Tanaka. The reason i selected him was because he was the pioneeer for developing mass spectrometry for biological macromolecules. A technique that has been inde forspensible my recent work 

Thursday, 27 February 2014

BBC Horizon - the power of the placebo

This season of Horizon has been a really strong one and "the power of the placebo" was no exception. The show not only established that the placebo effect works but that it can have genuine physiological effects. Fortunately they don't go into how a sugar cube has some kind of quantum channelling effect where it transports your mind to the memory of a pain-free life but rather how our brains respond to being fooled into thinking the placebo has a physiological effect.

Tuesday, 25 February 2014

Science exhibit plug

For those who are London-based and not actually involved in the event here's a great opportunity to meet some biologists in the flesh and get an insight into what they do for a living at the science museum.

There's an exhibit on Ageing, how Electron Microscopes are used and a silent disco (hopefully featuring songs that mention science) to name but a few. There certainly seems to be something for everyone.

So if you have the time - try and check out the Bio-revolution night at the Science Museum. I'm sure it'll be a lot of fun.

Tuesday, 18 February 2014

Schadenfreude for Scientists

Had a bad day at work? Angry at another grant being rejected? Well, you could always cheer yourself up at the expense of fellow scientists by checking to see who's made the latest paper retraction. There's a website dedicated to it called Retraction Watch.
Enjoy - unless your name is on it.

Friday, 14 February 2014

Name the Biologist

This Biologist is famous for developing a much-used technique in today's labs.

Bragging rights for the first correct answer!

As for the last installment, that was

Pacual Jordan. While he wasn't technically a biologist he was a well respected (at the time) pioneer of Quantum Physics. He was also one of the earliest proponents of the concept of Quantum Biology. Unfortunately Pascul was also a proud member of the Nazi party and this unsurprisingly led to his isolation from the physics community. It also meant that Quantum Physics was largely forgotten due to the fact he was the theories champion. It just goes to show that society and personality can often be more powerful than scientific ideas.

Thursday, 13 February 2014

Two days and counting to get a program installed on my computer.

Bristol University takes its computer safety seriously - some might say (eg me) too seriously. I wanted to align some protein sequences to see how similar they are and to do so there's a free piece of software that can be downloaded and installed. Usually it requires a click on "install" after download and within a minute the program is ready to use. Not so at Bristol University - I have to fill out a request for the IT team to grant me permission to click on "install". Two days later and nothing has been done - I'm not holding my breath that it'll be done by tomorrow either.
So thanks to a stupid system I'm going to lose a week wherein I could have done the piece of work instantly. Nice set-up there.

Fortunately a colleague who left has the program on his computer and as it is next to mine I'm using it. Otherwise this would have been a farce.

EDIT: On the quiet I've heard there's a relatively simple work around that I will test tomorrow. I won't say what it is for fear the IT gnomes find out and see fit to make life more difficult by blocking it.

Tuesday, 11 February 2014

Padawan Training

Imagine a Jedi wearing a lab coat instead of his cloak with their little padawan by their side (with ponytail).

That's sort of what I'm up to at the moment supervising a student's undergrad project. Whenever my PI mentions supervising students in the office I try and avoid eye-contact. Not entirely sure why but my knee-jerk reaction is it'll take me twice as long to do something I could do on my own. The odd thing is that when I do supervise students I wind up really enjoying it.

How come? Maybe I've been lucky in that the students I've worked with have so far* being competent and interested in their project. Most times I actually get them to do experiments while I do something else meaning I get twice as much done and that initial investment pays off.
I think that their interest is the key factor in why I ultimately enjoy supervising.  When I'm caught up in the day-to-day experiments  I tend to  forget that what I'm doing is still interesting and dare i say occasionally fun. When I have a "captive" audience doing experiments with me for the first time I'm reminded of how things work in experiments. A maxi-prep is usually pretty dull but when you explain what's happening at each stage and what you're ultimately achieving it's not so bad. When you explain how you get a fluorescent tagged protein into a cell-line I can't help but think  "this is a clever technique" (obviously not my own invention).

So it does require a bit more effort but it is a nice change of pace to have a student around. Let's hope I haven't jinxed things and that the current one doesn't go all Anakin on me - contaminating everything he touches and laying waste to my little empire.

*need to keep the current one honest!

Monday, 10 February 2014

Jim Al-Khalili - Quantum Biology Seminar

I've been a big fan of Jim Al-Khalili's for a while now. I think it was his TV series on the history of chemistry ("Chemistry: a volatile history) that "ignited" my interest in him and I've been a fan since. I like to think of him as "the thinking man's Brian Cox" which isn't meant to be insulting to Cox, as he goes for a much broader and younger audience but Jim's presentations are usually a lot more detailed and devoid of phrases like "stuff" and when he says "billions" he means it rather than it meaning "lots".

Anyway the University of Bristol invited him to give his seminar on quantum biology. It seemed like too good an opportunity to miss and I turned up 30 minutes early, eager to get a good seat at a full capacity talk.

As usual the talk was expertly delivered at a level that suited a university audience consisting of chemists, physicists and biologists. I think I found the history of the field the most interesting in the sense it can be traced back almost a hundred years which was news to me. A really interesting observation was how a champion and pioneer of the field, Pascual Jordan, essentially destroyed it by being an avid supporter and member of the Nazi party. Just goes to show how politics and society can have a profound effect on the advancement of science.

If I was being honest I'd say the meat of the talk discussing the potential examples of quantum biology in nature wasn't as impressive as the things he usually discusses. I think that's just because as a biologist I'm already aware and familiar with the examples he gave. I'm much more impressed when he's talking about pure physics but I guess that's just because the unfamiliar is more exciting to me. I'm sure there are physicists out there who find the biology just as fascinating.

One thing I did appreciate though was that he discussed some of his own research and it was nice to see he is still active in science outside of communicating it. It was also fun to see him get some in depth questions/grilling from quantum chemists in the audience and to see him defend his ideas. I'd have liked to pick his brains a bit more about his biological approach as I got the impression he was treating DNA as a molecule that existed in a vacuum whereas in life things get a lot more complicated (polymerases may auto- correct or the bulkier hydrogen atoms may be mutagenic through their increase in size alone). That said his basic idea of seeing whether DNA mutations can occur through quantum tunnelling is still interesting - even if biology itself may muddy these effects in vivo.

In conclusion it wasn't my favourite talk/presentation by Jim it was still an enjoyable hour and excellently delivered. He's still one of the best science communicators out there though and it was exciting to get a glimpse at Jim-the researcher for once. Well worth a look if he's giving the talk anywhere near you in the coming months.

UPDATE: It seems a few of you would like some examples of this Quantum Biology of which I speak. I forgot you weren't all at the seminar. Here are some links to get you started. If you want actual research papers you can probably pubmed it with the terms listed. Not all of these are excepted as fact yet but they are becoming very popular theories.

European Robin migrates via quantum entanglement
Quantum Theory of smell 
Superposition in Photosynthesis
Quantum tunneling in enzymatic reactions

and here are a few links that act as good introductions or reviews of Quantum Biology.

Sunday, 9 February 2014

Control Freak

The BBC has been on a roll  showing some experiments on TV of late - I'll try and cover Horizon's "fat vs sugar" . I stumbled across an even better example yesterday. The show is called "Inside the animal mind" by presenter Chris Packham  (who i still remember as the "really wild road show" presenter from decades ago). I was watching it mainly because i was curious as to see how animals view the world differently - something they achieve quite well. What I wasn't expecting was for them to be conducting experiments and actually explaining the concept of experimental controls.

I'll list a couple of examples

  • When testing whether a wolf or dog has a different hierarchy for responding to visual or olfactory stimuli - they had an experiment where food was present in two cups first then followed up with an experiment where the food was only in one cup. They also conceded the wolf used wasn't truly wild.

  • When testing whether strong magnets deter sharks (due to their magnetic sense) they placed tuna in the centre of a circle of strong magnets. In case the sharks were just apprehensive of black circles they had a circle of bricks (identical in appearance to the magnets) with tuna in the centre. These two circles were side by side - while the sharks repeatedly took tuna from the control circle, they never never took tuna from the magnetic circle.
There were several other neat little experiments where controls were mentioned or limitations clearly pointed out. They also liked to point out that n numbers are vital. The more times you conduct an experiment the more accurate the results become.

Basically my inner control freak was very happy with this show. There appears to be at least one additional episode so I look forward to seeing more experiments.

Saturday, 8 February 2014

Name the Biologist

I only found out about this guy after attending a lecture this week. He's an interesting character in that his political views actually set back a field in Biology by half a century!

And for those who can cast their minds back a few months - here's the answer to the previous installment.

It was Matthew Meselsohn and Werner Arber for their development of restriction enzymes (although they are famous for quite a lot of things) which are an essential tool for any biologist wanting to clone pieces of DNA into various useful vectors. I'd have a lot less GFP tagged proteins if not for them.

Tuesday, 28 January 2014

Lab Grab - Hunger Games

A member of the lab is leaving today. He has a cornucopia of kit and reagents we all desperately crave. Several people in the lab have already asked him "when can we start taking your stuff". We all know the time is fast approaching and we will have what is rightfully ours - at any cost...

I'd say his bench is far more dangerous than the arena - god knows what chemicals he has left on the surface over the last few years.

Sunday, 26 January 2014

A Great Biologist and an Exceptional Person

It seems even in death, Sir Kenneth Murray is still contributing to the future of biology with the details of his will being released. The BBC do a good job of covering the details of the will and of his achievements. It's humbling to think that the man who made a fortune from developing a vaccine against Hepatitis B chose to spend a lot of it on supporting science and training new scientists. There are several good friends I'd never have met if it wasn't for his (and his wife's) Darwin Trust - which is particularly good at funding non-EU students to obtain PhDs at the University of Edinburgh.

Thursday, 23 January 2014

Shame on you UK!

Here is a global map charting the outbreaks of vaccine-preventable disease.

Have a look and see how your country does and then ask why it may do so well or so poorly and whether your country actually has the ability to combat the disease effectively.

It's possible the UK's poor performance could be blamed on the NHS (although most/all of these vaccines are freely available) but I think the main culprit is the dangerous myth that the MMR vaccine causes autism. The fact that it remains can be blamed on a mixture of the media, the dissemination of facts by the government and academics and people's ingrained stupidity stubbornness.

So for what it's worth if you choose not to be vaccinated for these common diseases not only do you put yourself at risk but also all those who may not have access to the vaccine. So think of them.

I'm still waiting for a child who suffers permanent damage from a vaccine-preventable disease to sue their parents. It would make for an interesting case. I don't think it's happened yet and here are some links to some interesting discussions on the legality of the matter but it tends to concern other people's kids and not the victim challenging their parents.

Tuesday, 21 January 2014

Keep out

My boss had a great sign on his office door today.

"Writing a grant.
Do not disturb unless you have data on endosomal sorting"

I left him to his own devices.

Sunday, 19 January 2014

Lab fail

Since Christmas I've been cursing the fact that I've been sent a fly with a deleted gene only to discover a diagnostic PCR for said deletion reveals the gene is still there. I thought the fly may be on some "subtle" (the dreaded ultrabithorax*) balancer and that I was checking a heterozygous fly. I checked with the lab that sent the fly and they believed it was homozygous. Cue a lot of grumbling about people sending dodgy stocks.

The problem was that the deletion mutant would be really useful so I thought I'd design another set of primers because it just may be the case that I had got an off-target band that was roughly the same size as the band I was expecting. Desperate, I know.

The thing is when I got around to designing the primer I made sure I had the full info on the deletion as well. Eyeballing it, I thought "the deletion looks a lot bigger than the whole gene". That's when I realised I was comparing the genomic DNA of the deletion with the cDNA (the DNA that only encodes the protein). That's when it dawned on me that the primers I had designed for the diagnostic test were cDNA specific. The 1.5kb band I was expecting would be around 33kb from the genomic DNA. Never going to work with the PCR protocol I have!

So thanks to my ineptitude the deletion may well still be there. I've ordered the appropriate primers and will know by the end of the week whether it's real or not. Fingers crossed it is - I'd rather be an idiot than have to try and make a mutant from scratch.

*Ultrabithorax may sound like a really cool Decepticon but in reality is a really hard to distinguish phenotypical marker in Drosophila that only those gifted with "the sight" can easily recognise. The phenotype is present on the haltere of the fly which is like a tiny secondary wing that is used for manoeuvrability.

A) Wild Type  B-D) ubx130/Wild Type.  Figure taken from

You need to keep in mind that the haltere is very small to begin with.

Picture taken from

Basically I hate it. I'd love it a lot more if the marker was as penetrant as the homozygous mutant I'd love it a whole lot more because the phenotype is super cool.

Picture taken from

Da Vinci Dragonfly!  

EDIT: Fans of "Jonathan Strange and Mr Norrell" should appreciate the footnote to text body ratio in this post :P

Monday, 13 January 2014

Herbal remedies according to science

This has to be my favourite figures of the year so far. What with new year's resolutions I'm sure a few people have been looking into "supplements" as part of keeping healthy. Skeptics should take note that science is more than happy to say something works if they have evidence for it.
There's quite a few surprising ones on there for me such as Vitamin C not being that great for colds while Zinc is pretty good for them.

The nice thing about this figure is that it is constantly being updated so things could change as new results come out. There's also a nice section explaining where the information comes from so for the super skeptic you can find the actual studies and decide how "real" they are.