Game of Clones

A friend pointed this out today and thought it was worth sharing as it combines biology with Game of Thrones in a somewhat weird Biotech promotion.

I guess it's not a bad idea given that researchers probably have a higher proportion of Game of Thrones book/TV fans than the general populace.
It's not just for the pun and the above banner though. They go into far more detail. Each tool from their catalogue is placed within a "house" which comes with its own coat of arms and even a motto. If you can't be bothered with the link here is an example:

I think Renly would be inclined to take up the offer in house peptide ;)

The person responsible deserves a pat on the back for such an effort! Any american researchers should try and buy something if they can.

Science Songs

Inspired by this morning's wasted journey into the lab. Looking at the lyrics closely I can't help but wonder if Trent Reznor worked in research at some stage.

"it didn't turn out the way you wanted it to
but it didn't turn out the way you wanted it to
it didn't turn out quite the way that you wanted it

now you know
this is what it feels like"

Name the Biologist

This time we have two scientists with a connection in discovering something useful (they discovered other useful things but this one was a joint effort)

As for last week the mystery biologist was Alfred Russel Wallace who also came up with the theory of evolution via natural selection and was published papers alongside Darwin. The bizarre thing is that he was a major celebrity at the time but has been largely forgotten. Maybe a weird case of memetic survival of the fittest? Anyway these two articles do a pretty good job of analysing the man and why he has been forgotten. What can we learn from Wallace? 

•  If you want to be remembered you need to bring out a populist book rather than publish high impact papers - something that is probably very true of this era's "memorable" scientists.
•  Rushing your paper through when you realise someone else has scooped you always helps. 
• Being honourable and polite can often lead to you being forgotten.

Name the Biologist

This one is interesting as I'd never heard of the man before this week. It seems a classic case of writing a book gets you a lot more mainstream attention than publishing a paper.

As for the last instalment - the biologists were John Kendrew and Max Perutz who shared the 1962 Nobel prize for chemistry for their work on discovering the structure of heme-containing proteins. Perutz is the main reason I chose them for the quiz as he was (as far as I know) the first person to crystalise a large protein for X-ray crystallography and thus discover the structure.
I say "large" as is it was only in my digging around that I discovered the original developer of protein crystallography was actually Dorothy Hodgkin. She was a true pioneer in the developing the field (along with her John Desmond Bernal) and won the nobel prize in 1964 for solving the structure of vitamin B12 using X-ray Crystallography. I think I'll cheat and retroactively add her to the previous quiz.
Anyway the point is that X-ray Crystallography is an essential tool in the field of Biology and without it we wouldn't have a lot of major discoveries such as the structure of DNA and a lot of information on how drugs bind proteins or how viruses attach to cells. It still seems like magic to me so I salute those who understand it and especially those who developed it for use with proteins.

Pseudo-science, maybe.

I'm not a Quantum Physicist (and neither is Lanza) and I'd never heard of biocentrism but based on this article in the Independent about Professor Robert Lanza I'd say it has much to do with science as the spaghetti monster. What is annoying is that it uses his reputation in another scientific field and throws scientific elements into the discussion to give weight to his pondering.
The quotes in the article, "Death is a mere figment of our consciousness" and "the inescapable-life-matrix"  sound far more like philosophy or hokey dialogue from a science-fiction film.  There's a time and place for that but not in an article claiming a connection between science and the afterlife.
If he wants to be scientific about this the Professor needs to pose a question/hypothesis and design an experiment in which the results can be interpreted into statistically significant and reproducible answers. All this article provides is an hypothesis with thought "experiments" - things which we can all conduct in the pub late on a Friday night.

I'd also like to point out that being a well respected scientist in one field means your thoughts on another should be automatically excepted. From what I can gather the book is written by a biologist and an astronomer.
If I teamed up with an architect I shouldn't be taken seriously when writing a book on the language of dinosaurs.

I'd be interested to see how Quantum Physicists feel about the use of aspects of their branch of science. Surely there must be limits to it? Especially with the branch that considers infinite space or universes (I think the key is it's not universally accepted). An infinite universe/s is/are license to spout any crackpot theory because infinite is infinite. There are mes out there who will think I'm in the heaven and hell and limbo of all established faith systems. I'm also Batman somewhere out there and writing this very article upside down in the body of a chicken-fish, drinking wood whilst eating happiness and sitting on the back of a giant helium atom.

In fairness, I'm sure Lanza is fully aware of this and his book is not supposed to be a scientific document but treatise on an idea and maybe in the foreword of the book he explains he isn't presenting experimentally proven ideas.

Biology in Entertainment

I watched a recent episode of Agents of S.H.I.E.L.D that dealt with a virus that resulted in a person exploding in an EMP blast. Obviously that's a bit far fetched but there were some fairly decent examples of biology (for a TV show).

• They held a Gilson Pipette correctly
• They tested a cure on infected mice first
• They didn't try and use antibiotics! (I'm looking at you "Walking Dead")
• In an almost Sesame Street fashion they taught the viewers that you can't treat a viral infection with a vaccine but with an antiserum - the antibodies from a host that has been exposed to said virus.

They also used a centrifuge but they lose points for trying to make it more sexy with flashing lights (although I'd like one of those for a lab disco). They also removed the sample (which may or may not have been balanced) and then inverted several times which would make the centrifugation a little pointless.

Anyway I give this episode an overall thumbs up for Biology. I suspect physicists would not be so happy with how the skydiving scene could have ever happened.

Dance your PhD

An important aspect of Science is communication. We tend to do it via papers, presentations and posters but what about the medium of dance? Well here is a selection of brave and inventive souls who have tried to dance their PhDs. I'll let them explain themselves but a good effort and remember you can vote for your favourite.
I'm pleased this didn't exist while I was writing my PhD because while I can't dance to save myself it would have been just the kind of distraction from actual writing I needed. Not sure how I'd choreograph the role of Cdc2 kinase in acentrosomal spindle formation. Maybe after a lot of drinks at a science-related party we'd find out?

Name the biologist

This is a methods one and is pretty handy even if it seems like "magic" to me.

UPDATE: After a little more digging I discovered there's another Biologist who should be in this edition of the quiz. Apologies!

Last week's Halloween inspired answer is below.

Giovanni Aldini who may have inspired Mary Shelley's "Frankenstein". Much like his uncle, Luigi Galvani, Aldini believed electricity could be used to reanimate the dead. He just wanted to take it a step further from frogs to humans. He showed this could be possible with a public display of electro-stimulation of the recently executed convict George Forster. These experiments were occuring at the time Mary Shelley was writing. Besides potentially inspiring a classic book on the responsibilities of science and its applications he also contributed a lot to the understanding of galvanism and its role in living things.

Walking Dead Biology Fail

This concerns events in "the walking dead" season 4 and features one of my most loathed and prevalent false science assumptions.
There has been an outbreak of a virus in the show killing lots of their community. The solution - go get some antibiotics. The problem with this plan is that

ANTIBIOTICS DON'T WORK ON VIRUSES!!!

Control Freak

Sometimes I don't just obsess over the lack of controls on TV - I also like finding controls for mundane events in life. When the mild peril of "St Jude" threatened last week I had to put some new trainers on as my usual ones were wet from the previous night. My girlfriend suggested I should apply some waterproofing to them. I was skeptical so being a scientist I decided to conduct an experiment as follows;

a) Only one trainer was waterproofed, the other acted as a negative control.

b) It would be a blind experiment in that I wouldn't know which trainer was the test or control. It also meant I didn't have to apply the waterproofing.

I then walked into work and judged which shoe was the most wet. This was measured by looking at how much water was on each trainer.One had a lot of raindrops on it - the other had none. If "St Jude" had lived up to the hype I could have drained my socks into a measuring cylinder and judge wetness by volume of water from sock (assuming my feet are evenly sweaty).

Once I had the results I informed my "assistant" and she revealed which trainer had been waterproofed.
I can conclude that the waterproofing does indeed work. What's more tricky is finding a way to justify my girlfriend waterproofing the other trainer in the name of science.

*I assumed I didn't have some foot bias towards puddles but could have got around this by conducting the same walk with the waterproofing on the opposite foot (it would have to blind again). Of course I'd then have to assume there was the same amount of rain over the course of the second journey. A more controlled but less fun experiment would be to pour the same volume of water on each shoe and judge it that way.

Name the Biologist

This one is inspired by Halloween and he may have inspired someone else.

As for the last instalment - it was indeed John Tyndall. His contribution to biology was in finding a form of sterilization by creating "optically pure" air in which he rid a box of all air borne particles. He then found that food did not go off and concluded this was due to the removal of micro-organisms in the air. This backed up Pasteur's "germ theory" and his sterilization or "tyndalization" technique was used for some time.

This was pretty much an aside for Tyndall as he was a physicist at heart and was the first to come up with proof for the Greenhouse effect and an explanation for why the sky is blue. This last discovery, according to some (and Brian Cox), is the origin of the phrase "blue skies research". This type of research is curiosity driven where the scientist follows the results and/or whatever inspires their curiosity. This type of research can allow for discoveries that were never anticipated much like Tyndall's obsession with light and air particles lead to a sterilization technique (and a fireman's aspirator). These days funding agencies are far more happy to fund "objective-based science" eg cure a disease, build a fusion reactor making it harder for curiosity based scientists to get funding. Although with a little bit of inventiveness a researcher can make their research appear goal oriented )

5 Scary Costumes for Biologists

Halloween is almost upon us and while everyone else is dressing as Miley Cyrus and/or her wrecking ball, here are some costumes that will strike fear into the bravest of biologists.

Sweet Dreams Aren't Made of These

Had to get out of bed excessively early. Why? Because I was having a reoccurring dream where I was performing RNA extractions and realising I'd done something stupid mid-way. Things like realising I didn't have a glove on or I hadn't washed surfaces with SDS first. A particular favourite was discovering I'd put the flies and Trizol in a 10 ml falcon rendering it impossible to squash them with a pestle and then wondering if i could get away with decanting them into a 1.5 ml eppendorf.

It seems pretty sad when even my anxiety nightmares are science based.

As you may have guessed - I'm planning on doing RNA extractions later in the week. Hopefully these mental trial simulations will mean the real thing goes more smoothly!

Science Songs

By all accounts this was an intentional play on words by the band. "Selfish Jean" by Travis.

Name the Biologist

It's back, thanks to a little bit of inspiration from TV

This guy is old school and biology was just a small aspect of his scientific expertise. More importantly, his research style is one that many biologists have to wrestle with.

I'll put the answer up within a week.

Freezer Flood

Returning to work after a week and a half vacation is always tricky. First of all pretty much everything of use from my bench was stolen. Marker pens, tips, scissors, you name it. So I just went and took some more from another colleague who is away. The cycle is never-ending. A rational response would be to just make sure everyone has one of all the essentials but it seems to be a sport in my lab. On Friday I discovered that my bay area was flooded. Even weirder was the fact it was coming from the freezer that doesn't work so I've no idea how it managed to condense enough water to cause a flood. Almost as if it briefly came back to life just to annoy me. Not anymore. I've unplugged it. On the other hand the liquid nitrogen containers were dangerously low. I went to fill it up only to discover that both reserve tanks were also empty (see previous mantra). I took them down to be refilled. I'll check tomorrow to see whether they still need filling. I suspect they will.

The rest of the week seemed to involve repeatedly encountering the last of everything. This really winds me up but I guess the fact I don't personally take over ordering means I'm also to blame. I do try and adhere to the "you take the last one you order more" policy.

The "green" pipette tips have transmuted into gold as we don't have any more. This one is a bit odd as several people have claimed to order them and they've never arrived so I think that one is a distributor problem. The result is that a bartering system has now started in order to get our hands on tips within the lab. I'm also being super efficient with the use of the green tips. If I can use a "red" tip (10ul), I use that and gone are the days when I'd recklessly use a green tip for making mini-preps. I probably should count how many I have left every evening to ensure none of them are stolen. Hell, I should probably take them home with me every night.

Brian Cox's Science Britannica

I missed his last show as I thought it was a bit unfair how a physicist is taking all of science for himself in terms of BBC's science programming. This show is about Science in the UK though so I'll let him off as he's British and a scientist.

The first episode is about the perception of Scientist's as Dr Frankenstein and he posits where in British history the public fear may have arose and how it still remains to this day. He touches on the atomic bomb, GM food and animal testing and while those who are against all of those things won't be convinced I think he presents good arguments for them all to the general lay person and how scientists have a goal in mind rather than aimlessly "interfering with nature".

He also suggests that public engagement by scientists is the best way to combat the negative perception. The show makes good on this promise by interviewing several scientists involved in the controversial topics mentioned along with Sir Paul Nurse head of the Royal Society.

There are couple of funny moments. I liked how Brian giggles like a child when looking at a drawing of a horrible tumour from the 19th century. Then there's the staged "looking thoughtful on a train" scenes. My favourite moment though is one that I can only assume is the result of a dare. Brian is listing all of the big British discoveries in science which are popping up on the screen. The list includes, wireless telegraph, the first traffic light, jet engine, underground rail, the microphone, theory of evolution, the Christmas cracker, the structure of DNA and the discovery of elements. Does anything in that list strike you as not being that amazing? I'm not convinced the Christmas Cracker is in the same league at all. Maybe it revolutionised Christmas but it's not that amazing or useful.when compared to all the other things. Hopefully a tongue in cheek joke from the makers of the show.

I'll try and watch the other episodes and share my thoughts on them when I get the chance.

Science Music

For those of you who remember my post about performing climbing assays with flies (if not then have a look here) a song has recently come to mind as a potential anthem. It probably required a few months of repeating the experiment for the realisation to occur that Radiohead fits quite well.

Messed up layout

Sorry for the screwed up layout. It seems adding a twitter feed has caused the profile picture to turn into an invasive tumour that invades the "healthy" text tissue. I don't have time to get to grips with what caused this mutation so have removed the offending item and shuffled the picture to the right hand side. Think of it as surgery with chemotherapy - not a cure but a temporary fix. Hopefully the picture won't metastasise and get worse in the meantime...

Twilight Zone

I'm on vacation from Thursday so have the usual plan of trying to get some good results before leaving. I even popped in on Saturday to get a head start.

Turns out the PCR that was step 1 of my 3 day cloning plan didn't work (despite having worked fine on Friday). By then the sole PCR machine (we have 4 that don't work) was booked until the evening. So the plan of having my gene cloned into a GFP vector is out the window as I'm not so dedicated as to work overnight.

I figured I could still go ahead and seed some cells for immunofluorescence as an extra set of samples to look at during my confocal session on Wednesday. Cell line infected. No point in getting new ones as there wouldn't be time to do anything with them.

Oligos arrived for my fly cloning experiments. Unfortunately my cDNA clones haven't arrived and a trip to stores suggested they may be lost. So that set of experiments are on ice.

Fly crosses! No point - crosses set up now will have progeny coming out before I get back. If i set them up on Wednesday it'll be more useful. Otherwise I'm waiting for flies to get old.

So I've gone from having a busy couple of days to the twilight zone of not having much to do and there been no practical reason to start up other things.

At this stage I'm thinking I either shouldn't have gone on holiday or have started it 3 days earlier.

Looks like it good be a great opportunity to read relevant research papers and drink lots of tea.

Does Science (Research) Suck? - Possible Solutions Part 2

What other ways can the career of a Postdoc be made more appealing given a certain level of discontent at the moment? I don't have time for a silly and serious solution this time around so I'll leave it to you to decide where this one belongs.

Safety Inspection

We had a fairly big safety inspection at the University last week. There was a sense of dread and the usual "what a waste of time/ how inconvenient" rants. Our fear of being scrutinised was such that I couldn't help but get this tune in my head come the day of reckoning.

Control Freak

It only just dawned on me that I let "Dara O'Briain's Science Club" get away with not using controls in one of their experiments! I guess it's because it was quite entertaining. Fortunately my anal retentiveness resurfaced and I can now call them out on it.

So towards the end of the "invisible worlds" episode they were demonstrating how effective a "hydrophobic" spray was on waterproofing objects. They tested a trainer by pouring water over it and an iPad by submerging it in a tank of water. The water bounced off the trainer and the iPad continued to work underwater quite happily. Amazing stuff but without the control it's meaningless. How do we know the trainer wasn't waterproof without the spray being added? How do we know iPad's are so well made that they work under water? With a control, that's how.

So the experiments should have been like this (as a minimum);

A pair of trainers; one sprayed with the hydrophobic can, the other not sprayed at all. Pour a jug of water over both of them. If the unsprayed trainer gets wet we know the spray works.

Two iPads; one sprayed with the hydrophobic can, the other not sprayed at all. Place both of them in the same tank of water and see whether they both shut down or stay on. Any difference can be attributed to the spray (or lack of).

Now I can understand them not wanting to kill an iPad  (especially as a licence fee payer) but the trainers would have dried off eventually.

EDIT: If a video of it turns up on youtube, I'll link it. There isn't one at the moment at the iplayer clip will shortly expire.

Dexter's "science"

Sometimes in TV spectacular science is presented as mundane while standard science is presented incorrectly. Here's an example.

During a recent episode of Showtime's "Dexter" some "science" was deployed. After all, Dexter is the lab (Dexter's laboratory :) ) technician in a police department. In the episode he managed to get some DNA from the killer at a crime scene - to their credit they did point out the hair was pulled out by its roots (most TV shows seem to get DNA from hair clippings which is pretty impressive). The DNA database didn't give him a match but he then decided to go for the mitochondrial DNA in the hope the mother may be on the database. With the click of a button an instant match came up.  It conveniently belonged to someone he knew so his next logical step was to get a photo of this woman's child. Once scanned into the computer he used a "magic" program (which could still be indentified as photoshop) to add 30 years onto the 6 year old child. Hey presto it churned out a picture with a 97% match (no idea what stat was used) to ANOTHER person he just happened to know.

Pros: They know you need roots of hair to get a DNA sample
         They know that mitochondrial DNA is inherited from the mother.

Cons: I don't think you can age people on computer software that quickly or that accurately.
          I don't think you can sequence DNA and do a search that quickly either.

Dara O'Briain's Science Club

This one has passed me by largely because it's in a weekday time-slot that doesn't suit me and then I always forget to check it on Iplayer. In typical fashion, I managed to catch an episode only to discover it's the last in the series. Bit of a shame as it's actually quite good.

Science Songs

This song popped up on my mp3 player and I'd never considered the relevance to science. It definitely feels like a song about a project that isn't working!

These Wooden Ideas by Idlewild;

"I bet you don't know how to sell Conviction" - those talks are always the toughest...

The Guardian's "20 Big Questions in Science" - Biology FTW!

The Guardian is having quite a good run of late with a broad range of interesting articles and I applaud anyone giving people a daily dose of interesting science to people :)

This one tackles 20 of the big questions in science which covers cosmology, physics and things that very much concern us. Any of them would make a good platform for a sci-fi tale (may of them are already staples of sci-fi eg time travel).

Does Science (Research) Suck? - Possible Solutions

Continuing the post about researchers disillusionment with science, I thought I'd be proactive and make some silly/serious suggestions for how things could be improved.

Control Freak!!!

I'm going to try and post these whenever I encounter them. One of my gripes, as a scientist, is when anything is presented as a "scientific truth" but lacks the most basic of scientific principles - a control.
Without a control you have no idea what is actually causing an effect or whether the effect is merely the result of the experimental procedure itself. If your test is different from your control(s) then you can claim there is a significant difference.
I've touched on the subject before and think it's useful to try and point out other examples. It should hopefully appeal to the anally retentive scientists who read and help make non-scientists aware of the concept and allow them to be a little more cynical of "facts" that are presented to them on TV/media.

Does Science (research) Suck?

There is a great little article on The Guardian site where Kayleigh Dodd highlights issues that a lot of research scientists share. Myself included.

Kayleigh points out the plight of a research scientist is that they have a very limited shelf-life of about 8 years after their PhD where they essentially have to become a group leader or get out. The problem is that regardless of whether every postdoc were to publish yearly in Nature and/or Science they aren't all going to get their own lab. There simply isn't enough money, especially in the current climate, to allow for such exponential growth. So that leaves the vast majority of postdocs in a situation where they aren't going to be group leaders and therefore have to leave academic research and hopefully find some other career because permanent postdoc positions or senior lab manager positions are few and far between. So unless we have a scenario where everyone naturally moves into another job of their own choice we seem to have a pyramid scheme that throws you off if you don't reach the peak in time.

An institute for evil science!

The X-men: Days of Future Past PR machine is off to a great start with this Trask Industries website. It does feel a lot like a pharma/manufacturing website and I love that it uses graphs! the icing on the cake is a mention of Thomas Hunt Morgan and his genetic studies in Drosophila as a bench mark in their alternate history in genetics :)
It also seems like they are applying a pseudo-scientific approach to mutants by describing low-threat mutations (multi-coloured eyes) and high threat mutations (shape-shifting, telepathy and super strength). The wiggle room for such a variety of powers as the result of one gene is that the "X-gene" affects gene expression on a multitude of levels. Nonsense, of course, but genetically "sound".
They also seem to try and make plausible the concept of mutant detection and suppression as well. It's well worth a look!

The question is would I work for such a company? Well, if they offered me a good salary and didn't base my work on paper publication (but X-gene innovation) and have permanent positions for Postdocs, I'd probably consider it given the poor alternatives. I'd have to check the small-print on whether being Ginger was a high-threat mutation first.

I've heard rumours that a millionaire called Warren Worthington III has a more benevolent research program under the supervision of Henry McCoy. Maybe they can make a better offer, I'm sure my knowledge of Drosophila genetics could come in useful.

The "hit" list

There is something decidedly sinister about this "updated" lab members list.

Feels like a scene from some serial killer blockbuster. Thankfully, I'm not on the list but I fear for those who are. I think an updated new list would be better on pretty much every level.

Hung Out To Dry

I noticed this in the stairwell at work today and was struck by the visual simile :)

Note: Not that the metaphor is directly associated with the person who made the poster!

Temperature Sensitive

There has been a statistically significant span of "hot" (in comparison to British controls) weather in the UK for the past 2 weeks.

At first this rare occurrence is welcomed with national glee but after a week the media decides it has to be a sign of the apocalypse and issues weather warnings. The British also discover they have no small-talk when the weather is consistently good and so have to find things to complain about.

It makes me wonder whether there is a temperature sensitive mutation that occurs to denizens of the UK where after temperatures exceed 27 degrees we can no longer function? This would make sense if the UK was an isolated nation with a narrow gene pool but we aren't. This leads me to think there may be some kind of retrovirus that only exists in the UK. Upon infection it rewrites our DNA to be useless in warm conditions. This must be a virus that can only survive outside the host at temperatures below 27 degrees. I guess it makes sense that it would program the host to seek out mundane temperatures so that the virus can propagate.
The virus may have other personality-altering functions such as encouraging heavy drinking (a feature that is probably always being expressed). This could suggest the virus spreads via beer glasses or badly maintained urinals. It would also help explain it's prevalence in the UK and not other parts of the world.

I've never heard of a case of a virus being able to infect metals but I am starting to wonder whether this may be the case. Afterall, I can't understand why railway tracks become "unstable" in the UK at temperatures above 27 degrees. If this was true of all steel then surely huge parts of the world would be back to horse and cart or cars throughout their summers?

So I think this would make an excellent grant proposal to try and isolate this amazing virus. Not only could it help us under stand host behaviour modification but it could also be a breakthrough in materials science. It may be years away but imagine how nice it would be during the next heatwave (probably sometime in 2025) for the British government to provide an immunisation program against this virus (assuming it doesn't change us on a DNA level). Maybe then it would be possible for us all to enjoy the weather?

Of course we could just avoid the news while the weather is nice.

fly in the ointment

Some afternoons just don't go to plan and this was one of them.
All set to do a GFP pull-down on 10 plates I'd transfected on Weds only to discover 2/3 were infected. That's that experiment in the bin.
I then found out that most of my other cells were also infected. It could have been lousy technique but apparently most of the lab got an infection late last week which I didn't know about as I was at a wedding.

Nevermind, I'll go and set up those fly crosses I was planning on doing. Tipped 50 odd virgins out only to find a male fly in there with a wide grin on its face. Because I could no longer be certain they were virgins they were useless for crossing so they took a plunge in the ethanol bath.

At this point there wasn't really anything else to do and being a bit superstitious decided there was more chance of it working if I do it tomorrow.

The morning went ok with 24 mini-preps. The downside to that was having So Solid Crew's "21 seconds to go" stuck in my head, changing the lyrics to "24 preps to go"

Not quite "The Fly"

So this is what an assay for locomotive ability looks like. I'm a bit more careful with them when doing the actual experiment but you should try filming with one hand a whacking flies to the bottom of a tube with the other (I can see that sentence being misquoted).

For added benefit check out the sound effects. That weird drone is the sound of the carbon dioxide being pumped out to keep the flies unconscious (and probably myself soporific). The really unpleasant sound is Radio 1 playing in the background - possibly the cruelest thing the flies are subjected to.

Now I need to edit it so that it looks semi-professional in my presentation. The moving pictures may distract the audience from the less than stellar results.

Don't worry, I'd never try and submit that as supplementary data in a paper.

Swamped

I am still here but work/life has been pretty busy the last month and will remain so till July. This week I have a departmental talk to do which I have yet to start but have been busy pushing for data on it.

Today has been a case of trying to get stats to show something meaningful which always sounds dubious. The problem I have is that while I can show significant differences between genotypes, I can also show significant differences within genotypes rendering the whole thing a bit pointless. Although there is one obvious outlier that is literally putting a fly in the ointment. Or ointment on the fly in this case.

I fear I will be having nightmares about spreadsheets tonight.

An Anthem for Bad Results

A colleague of mine got the results back from a pet project he was hoping to expand upon when he has his own lab. They weren't very promising and he pronounced "The dream is over".

I instantly wanted to say "Hey now, don't dream it's over" which resulted in this song being stuck in my head for the rest of the day.

As it turned out he got some more results in the afternoon that meant the dream wasn't over. A happy ending.

If I wasn't so self-conscious of my atrocious singing I think I'd be tempted to break out into this whenever a colleague is feeling defeated. Although they may think I'm taking the piss, which I might be.

What's my age again?

I turned 32 last month and have to admit it’s becoming harder to deny I’m getting old. The emphasis on early in “early thirties” is reaching its limit and I think it’s time to reassess what my age actually means in an attempt to sound younger.

Communication Breakdown

A friend of mine is giving a departmental talk this week. An email was sent announcing their talk which had the title;

"Splicing factor, histone modification enzyme, and transcription factor that are required for transposon silencing in Drosophila goatees"

This was pretty exciting as I've never noticed that flies have goatees but perhaps this was an amazing mutation or the result of a splicing factor, histone modification enzyme and transcription factor working in conjunction to create a goatee?
Maybe it would look something like this?

Science Music

AlunaGeorge's "attracting flies". Funnily enough, I noticed this while changing my fly stocks. I should point out that Drosophila Melanogaster aren't attracted so much to the thing she is alluding too (well I've never tested the possibility in the lab to be honest). Unless she is accusing someone of yeast breath? Could be an alcoholic or bread addict I guess.

Anyway, it'd be a potential choking hazard if the subject of her song worked in my fly room.

Science Music

This isn't really about science but I'm in the process of assaying Drosophila motility as they get older and whether my mutant is worse than the controls.

The assay looks a bit like this;

I'm sure that having seen the video you can appreciate that the following song has taken root in my mind and become a soundtrack to the climbing assay forever more.

The 5 second rule - tested.

The BBC made a nice little video "testing" whether the "5 second rule" had any merit. Here's the video (not sure if outside UK readers will be able to see it?)

http://www.bbc.co.uk/news/magazine-21945313

Basically it's not a good idea as the food samples dropped on the floor for 5 seconds all had a lot of nasty bugs on them after culturing them overnight on bacteria friendly plates.

 Fortunately the "mum" points out that the cleanliness of your own floor is also an important factor.

There is one flaw with the experiment though as they don't have a true negative control - unless I'm misunderstanding their "0 second" test. Basically they need to put a sample of bread (or apple) that hasn't been dropped on the floor. It could well be that the culture results are from the food itself and not the floor. They could also do a floor imprint as well while they are at it. If there's as many cultures on the plate for the sample that never contacted the floor then the contamination is inherent in the food. In which case the 5 second rule still applies! There's still hope.

Still a commendable bit of everyday science on the BBC.

Throwing the baby out with the bathwater

I had a bad headache at work yesterday and it's clear mistakes are made when distracted. In this case I was running digested vector and DNA out on a gel to purify them. When I looked at the samples there didn't seem to be a band for the DNA in my vector digest so i threw it in the ethidium bromide cookie jar. Then I realised an empty vector wouldn't have the DNA in as that's what I was attempting to make. So i fished the gel back out the trash (don't worry it was at the very top) and cut out the digested vector bands.

I then decided to take a lunch break in the hope my head would clear up.

The headache didn't clear up but, when I got around to the ligation, I realised I should have cut another two bands out of the gel as well. There was no going back to that gel as I had already eviscerated it.

Guess I'll be repeating that one again. My headache seems to have gone so any additional cock-ups are solely due to ineptitude.

put that in your Pi(pe) and smoke it

"Person of interest" is a show i find quite enjoyable. It doesn't have much to do with biology and a lot to do with a crime fighteer kicking-butt based on numbers a super computer gives him. I recently caught an episode which has an excellent answer to the "what's this useful for?" question that science teachers are frequently confronted with.

That's a pretty good come back, It also reminds me of the creative license that infinite provides. Somewhere in Pi is the conclusion of "A Song of Ice and Fire".
And this post.
And the next one.
Etc...

Yo Mama

Zach Wiener posted some excellent "yo mama" jokes for nerds. The full list is here but I'll quote the two biology ones.

"Yo mama's skin is so lumpy, the bacteria on it experience allopatric speciation"

and

"Yo mama's so scientifically illiterate she thinks ATP is where an indian live"


I'll try and think of one of my own but ATP sets a very standard.

Harry Bioblogist and the time-travelling Gilson

I had a very odd dream the other day, suggesting I'd possibly been working too hard or not doing enough non-science things. It went a bit like this;

I was in the lab and discovered that my Gilson pipette could allow me to travel through time.

I guess if the "Doctor Who" franchise had a timelord called "the scientist" (would probably make a fun villain) instead of a "sonic screwdriver" he'd have a "temporal pipette".
There were rules to this time machine though. Instead of measuring out volume in microliters it measured time in years. It was a P1000 so it meant I had a thousand years to play with. Where the dream became dull (and indicative of too much work) was that rather than use it I thought about how I could use it. The assumption in the dream was that it would take you to any time from 0-1000AD. I was hesitant to use it, as I'd have got trapped in the past, but now I'm thinking the tip-ejecting button would return you to the present.

Anyway it seemed like a fun idea and possibly a bit too science oriented for a mainstream audience. If this was to be adapted into a "major" series. The temporal pipette would work as follows.

1) Set the date by setting the "volume"
2) Travel back in time by pressing the suction button in
3) Return to the present by pressing the "eject" button.

Alternatively for more flexibility the 0-1000 setting just represents the years travelled. pressing the suction in (after setting the time) goes backwards and pressing eject lets you go forward.
Clearly there's be a huge advantage in tracking down the P2000, P200 and P10s as they would give a larger range and allow for much more specific travel.

What other lab equipment could have magical sci-fi powers?

If a centrifuge was big enough and you could climb into it I'm sure it could spin you into another dimension. MASSIVE DISCLAIMER - DO NOT TRY THIS AT HOME OR IN THE LAB.

100th oligo!

I ordered my 100th oligo since starting the new postdoc today. They've been used for placing GFP on my genes of interest, making recombinational knockouts, checking things are where they are supposed to and hopefully confirming things aren't where they are supposed to.

Can't say they've all been useful but some have served their purpose. Let's see how long it takes for the second century.

This week in the lab (part 2)

So I left you all on a bit of a downer last time. Trust me, it was worse for me and I had to wait 3 days for some positive news.

On Monday I sent the gel with SILAC samples on for mass spec. analysis. SILAC sounds terrifying but it's really very straight forward in principal. The key thing is that arginine and lysine can be produced as heavy isotopes - the amino acid is the same it's just that they are made from heavy stable isotopes eg deuterium, 13C and 14N. If you grow your test cells in heavy media and control cells in light media then you have a way of telling them apart (with mass spectrometry). Here's a diagram that I hope illustrates the experiment.

Simples?

I was really lucky in that I sent my sample when there was no backlog of samples and got my results back on Friday morning, rather than in 8 weeks time.
I (or more accurately in conjunction with colleagues more familiar with this interpreteting) need to pick through the results tomorrow. An exciting hit is for a protein connected with a human neurodegenetative disease (ND)
Now, it's well known that you're only ever one experiment away from destroying your project but this is exciting as it actually gives me something to work with and that's exactly what I needed.

I think it's called "hope"?

The fact there may be a potential link with a human disease is a generous dollop of icing on the potential cake.

The other potentially good news is that the only mutant I have, the viable one, is the mutant for this gene. It could well be that I haven't even spotted any movement problems in the mutants and I certainly haven't been looking at their brains. Now I have a reason to look closer. It might also have no phenotype in isolation.
The first priority is to confirm the interaction which I can do in several ways, such as;

1) Confirm I can pull ND protein down with "MyProtein". This only confirms a physical interaction though.

2) Confirm a genetic interaction. There are models of the ND in flies and I can use this model to see if "mygene" mutant modifies it. This would be even better as it would confirm there's a physiological interaction and whether it is a positive or negative regulator of the ND.

If test number two works then things are looking up. If not, I may be back to square one or looking at some of the other hits from the interactome. Let's see what the next experiments bring...

EDIT: Censored on the off-chance it's giving too much away. Damn paranoia about being scooped, but you never know. It costs people their jobs so I shall remain secretive until it turns out to be a waste of time, I publish it, or someone scoops me anyhow.

This week in the lab (part 1)

This week managed to capture the highs and lows of research.

On Tuesday my PCR suggested that I had an ideal mutant for "Project4". Basically the P-element gives the fly red eyes and when the P-element leaves the fly has white eyes. Sometimes when the P-element leaves it takes neighbouring DNA with it and can create mutants. The process is random and has to be muscularly confirmed. I began by screening the lethal candidates, as they are most likely to have a mutation - what with them suddenly being dead. One of the candidates looked like this;

All well and good as P-elements are only supposed to excise in one direction meaning "not that way" gene should be intact. However, I decided I should check this, just in case, and because i also wanted a stretch of DNA that covered the mutation for sequencing. This is what happened;

What the hell? So much for that theory of it only deleting in one direction. This is bad news as I have no idea whether the lethality is due to a mutation in "project 4" or "not that way!!!" gene. I'd have to put "not that way!!!" back into this mutant to show the effect was due to loss of "project 4" - if that is even the case. "not that way" gene is a polycomb related gene so it's easy to imagine it could be essential.

This pissed me off quite a bit as it's the second really iffy P-element excision I've had in this lab. The other mutant I've made for "project 2" is what I like to call the "quantum mutant" as it can only be observed indirectly. Basically the P-element is still there when tested indirectly but isn't there when I test it directly. "Project 2" and "other way please" gene are intact but the line is now lethal. The original P-element line is viable...

At this stage I wanted to knock all my fly stocks off the table in a "Bill Adama, wrecking his model ship/painting" rage. The only mutant I've made that makes any sense is viable  and it's hard to drum up excitement for a gene that doesn't appear to do anything. A similar thing happened in my previous lab but I was at least able to confirm it mutated the gene I was interested in. Why does this keep happening?. A little bit of investigating revealed that all of the dodgy excisions I've made are ones that use the "Epgy2" P-element. It seems this element takes a perverse joy in screwing you over with confusing results. It also seems to have a tendency to lose the white gene without losing the P-element, so beware if you are doing an excision with it.
Honestly, I think it's time i try some of the new mutant making techniques. Not recombinational knockout as that seems like a ball-ache too. TALENs seems to have potential.

And that's the bad news for the week. I'll leave you on the cliffhanger of the good news until tomorrow (because I have stuff to do now).

Fire Drills

Fire drills are essential for large buildings but they can be a massive pain in the ass and potentially disastrous when researchers are "surprised" by a drill. If you are in the middle of a massive experiment that can't be put on hold or you have got that slot on the confocal you have waited a week to get then a half hour drill can really ruin things.

Valentine's day for Biologists

Being a scientist can be lonely, with little time for love - outside the love of science! To prove that we are still capable of emotion (and pattern recognition) here's a few pictures I found via a quick google search. In the true spirit of science I'll also tell you what they really are to dispel any undue sentimentality,

This one is taken from Helen Jacques and is a picture by Mathieu-Benoit Voisin and Doris Proebstl from London. "The researchers are studying how white blood cells move from the blood into into damaged tissue to cause inflammation; for example, after a heart attack. They were using using fluorescent pigments to stain two key players in this inflammatory process – pericyte cells from the blood vessel wall (stained red and blue) and collagen (green) – when looking through the microscope they noticed that the cells had arranged themselves into a heart shape"

This one is cheating a little but it's animated. You have to go to the web page to see it though.

This one is sweet...

That's the effect of tuberculosis in the lung of an infected mouse.

I guess the take home message is that scientists get bored when spending hours on a microscope and that horrible diseases can at least look romantic while they are infecting or killing you.

And let's not forget what the real thing looks like.

 Happy Valentine's day!

SILAC'S BACK! :)

For those of you who couldn't bare the cliffhanger of my last post, here is some good news - the cells seem to have clawed their way back and are now looking good for being confluent before the media is exhausted.

Phew.

Other decent news is that my antibody and the siRNA works. Ish. There's 3 bands, two of which disappear with siRNA but the strongest band not so much. Antibody for gene2 doesn't appear to work and instead looks like a dirty smear. This is the reason I didn't check the results until today. If I'd seen that at the weekend I would have felt the time spent there at the weekend was for nothing and have called it "bad" news. On a Monday I'm more prepared for things not working, hence this is "decent" news.

Are you confluent? Not nearly confluent enough.

On Friday I had to decide whether my "super-confluent" cells for my SILAC experiment were superconfluent. Unfortunately the lab "Aragorn" wasn't in to advise me and it looked like a do or die scenario. After consultation with other members of the fellowship lab it was agreed they were confluent enough and that they may die without more food. So I went ahead and split them.

I was in at the weekend and the king had returned. I told him about the scenario and he told me they weren't confluent enough and chances are the media will be used up before the cells are confluent again. As we are awaiting more SILAC media it could be the experiment dies.
"Aragorn" warned me; "A little more caution from you; that is no trinket you carry"

Now I just have to cross my fingers that those cells make an amazing comeback over the next 5 days.

Throwing the Baby out with the Bathwater

Started a SILAC experiment which i still maintain sounds like a great name for a villain, preferably a cyborg one. I've been told repeatedly that it's quite an expensive process so I was very focused on not screwing it up - so much so that I forgot to think about screwing up other things. Case in point I was splitting my cells, with gene-GFP stably expressed, into the SILAC medium and forgot to keep some of the cells for maintaining a line with.

Checked the -80 stocks and I didn't have any left so I'm going to have to reinfect the cells. Logic dictates it worked the first time so should work this time but experience dictates it probably wont be that straight forward.

The SILAC experiment remains on track for now though.

I'm still giving my flies the silent treatment due to their refusal to show a phenotype and for the P-element excision giving utterly bizarre PCR results that make no sense whatsoever. I'm starting to think the gene may be the gene for using quantum mechanics as it can only be observed indirectly as a null but never directly.

When Lab Colleagues Leave

A colleague from the lab left this week. He'd accumulated quite a lot of kit over the years and as he was tidying up on Thursday the rest of us began circling like vultures trying to find the prime pieces of meat for when he left. I actually cheated and asked him if I could have some of the boxes.
He officially left on Thursday and I think if there had been a time-lapse from 6pm Thursday to 11am Friday it would have looked a little bit like this (don't watch if you find decaying animals upsetting).

On one hand it feels a little disrespectful removing a person's stamp on the lab but on the other it's good that we recycle equipment and don't waste money buying new stuff all the time. The other perk is that there is a little more room for me to use now as I can use his bench to do stuff when mine is cluttered. The only downside is that the only other person in the bay area will also be leaving in a few more months and then I'll be all alone in my domain. Unless someone else joins the lab and then I'll have to start scent marking centrifuges, fridges and freezers.

Good luck to Colin, with whom I was able to share many silly scientific flights of fancy. I will remember him whenever I use his scissors, large Gilson and stopwatch.

When lab meetings go well

Had to give a lab meeting this morning which meant a decent chunk of the weekend was spent preparing one. This was particularly difficult as I feel like most of my projects aren't really going anywhere and the fly side of things feels reminiscent of the phrase "throw enough 5h!t at a wall and something will stick" but with a frictionless wall.

Anyway, I decided to tell things as they are and suggest I should maybe focus more on tissue culture for the time being as that has the greatest potential of turning into a paper at the moment. The flies can come into it later once the biochemistry gives me some targets to home in on.
The great thing about the meeting is that the rest of the lab were keen to offer suggestions and help with various experiments that should move the cell culture along and I came out of the meeting with at least 3 experiments to do and a plan of action to keep me busy for the next month. One good thing about being the "fly guy" in a lab of tissue culture and biochemists is that there is a lot of knowledge to draw from.

It's always a good meeting when you walk into it on a low and come out of it, enthusiastic about beating the project over the head in a variety of (hopefully) productive ways. Thanks to the PI and the rest of the lab :)

Sometimes you have to be really careful labelling things.

There were two events at work today where I realised you have to be really careful when writing things down. the first was fairly innocent. I was using primers for PCR. One of the ones I wanted was "NJP082" but that's a squeeze to write on the top of an eppendorf so I settled for "82". Unfortunately I then discovered a "28" and I don't numerically categorize the diluted oligos...

I will try and remember to get a photo of this to prove the problem. For now, here is an example - keep in mind it's a lot smaller when on the top of a PCR tube.

I did a little bit of detective calligraphy and was able to work out which one was which but decided to make up a fresh dilution and underline it this time around.


The second issue was more problematic

Splice - Movie Review

Splice is a 2009 science fiction film directed by Vincenzo Natali (all the pertinent info can be found on wikipedia). Given it's about biologists creating an artificial chimeric life-form I thought it would be worth a look.
To my relief the film isn't actually a horror film despite the trailer being edited to make us think that.

Humans have special powers!

Sometimes a research headline pops up where you think "What a pointless question" only to find out it's answer is potentially quite interesting. This was probably the most involved I got in the discussion of science at work today.

Scientists speak the truth

Twitter is having fun with #OverlyhonestMethods  at the moment. This site collects some of the best ones too.
I think it's a good thing that scientists are being a bit more open about why they do things in experiments the way they do. It makes us seem a bit more human and fallible.

If I were to admit to some they'd be along these lines and I suspect they'd be true for a lot of biologists.

• Flies are kept at 25 degrees because then I don't need to come in at weekends.

• Secondary antibodies are left on the sample for 2 hours because sometimes I like a long lunch or a quick drink in the evening.

• I worked on a project because the wings looked fat (short and round) and not because they looked like Fat (protein knock down). Luckily it actually did interact with Fat. 

• I do X method because that's how it worked - I have no idea why it worked and honestly don't care that much.

• I use euparal fixing method because you can order it, rather than make it and it smells nice.

• When I try to summarise a method with the phrase "basically" you can guarantee there's nothing basic about it.

• sometimes I find an interesting result by accident and then have to concoct a legend as to why this was what I was expecting to find all along. 

•  when a method says "72 hours" later I tend to do 10 or 14 as staying at work until 9pm or starting at 7am is too painful.

If I was being overly honest about this blogpost I'd say "I wrote this post because I don't have a twitter account and can't be bothered setting one up right now"

Happy New Year!

Hopefully 2013 will bring a more regular schedule on the site with some of my science, some of other people's science and the general silliness. I have to admit finding new "name the biologists" is getting trickier with time but there are 1000s out there so I just need to think more carefully.

One thing I've discovered is that Flies really don't care if it is a bank holiday. Those little sods are going to need collected, tomorrow at the latest and I have a host of virgin flies to collect if I want to try and establish some mutant lines.