Saturday, 31 December 2011

Happy Holidays!!!

Wishing everyone happy holidays and all the best for 2012!!!

Tuesday, 6 December 2011

Ticked off - and really happy!

As scientists our jobs involve a lot of project management: I myself at this moment am running three projects within one umbrella project, and this requires good organisation skills, good time management and note keeping.  Note keeping I would say is the most important, and although I am the first to admit I am not perfect: I have recorded notes in pencil instead of pen *gasp* - but only because I had lost my pen down the back of the bench - and I scribble and scrawl instead of, er, write; I do make an effort to get everything down of what I have done that day - what the outcome was and what I am going to do next.  I cannot describe how frustrating and sometimes how nerve-wracking it is, while you are setting up a complicated experiment - that may have to run its course overnight or over the weekend - for you to get distracted for one tiny second and forget what you have just done, or just added!!! At this point you have two choices: you can either throw it all away and start again - and waste materials (possibly some of which you have had to meticulously prepare yourself) and time and money, OR, you can continue, hoping that you have just done what you thought you had done right,

.......and spend the rest of the evening or your weekend biting your nails off.

SO ALL HAIL THE GREAT LAB BOOK! (Or laptop, note pad, ipad, whatever you prefer), the great keeper of reaction mixtures! - where every ticked off component is a swipe of  relief and assurance that it has been truly added and is contributing to your experiments success! (Or you'd hope so).

Yes, note keeping is important, and in this job it can be a very reassuring and pleasing to be ticked off all the time! 

Scientist gets hen pecked by wife for not taking a better paid job

With global recession apparently looming next year, I thought it would be a good idea to check out some TV programmes that could provide some good useful insight on how to deal, sensibly, with money.  On BBC2 (UK) there is a fairly new series dedicated to the subject, with the first episode based on taxes: who pays what, who doesn't want to pay what, and how much in terms of benefits do we get out of it all (incidentally, national insurance is the same thing as income tax! I never knew that!!!)  This weeks exciting episode was on couples, and tonight a group of them were invited to discuss their issues with their shared finances (oohhh, I said, elbowing my partner, this is interesting!)

All the couples came from very different backgrounds and had very different views on the subject, but my attention was caught by these two:

She works in a lawyers office and he works as a researcher at Manchester University; he is the breadwinner.  They have a very nice house, a nice family and seem pretty well off, but she is not happy.  She states that her partner is tight with money, is paranoid and that "all fun is banned from this house!" In front of the camera and with her red-faced partner beside her, she criticises his selfishness; that while he is doing a job that he loves, he is causing "suffering" to their children in that his pay check does not bring home enough to guarantee them a good future.  She wants the children to go to private school, she wants bright futures for them, and having seen the people in her work place earning triple the amount he does, she wishes for him to retrain for another profession, like accountancy : "Someone of your talent will have no problem doing that! Most of the general public do jobs they don't want to do for money!"

It is stated in the programme that the man earns £34,000, indicating that he is probably a senior post doc.  The salary is above the national average, but with children, a mortgage and other bills to pay, that really doesn't amount to much, so is his partner right?  The poor guy stresses that he loves his job and that he can't see himself doing anything else, but is that enough?

More and more scientists are realising that obtaining tenure and funding in academia is becoming increasingly difficult.  Even if we love our jobs there may come a day we have to find pastures new.  But is our passion all for nothing? Is our efforts all in vain? As mentioned in my previous blog Fat cats and dead rats it seems that academic science is the only profession where its professionals are treated so poorly in terms of job security, pay and benefits.  Should we become more selfish (or selfless, for our families as in this case)

....and all become accountants??       

Sources:  BBC2 Money: Couples



Tuesday, 15 November 2011

PhD in burger flipping!! No, seriously...

As reported last night in A Brave New World with Stephen Hawkings and in Sky news today, science is taking a turn towards the culinary, with scientists looking to create the world's first lab-created burger! In answer to growing world hunger and to reduce the ecological impact of farming meat-yielding animals worldwide, Mark Post at the University of Maastricht is aiming to grow cultures of meat cells dervived from meat leftovers from slaughterhouses.  These cells at a certain point will then be seeded onto collagen fibres where they will grow to form strips of meat.  The muscle strands, like in nature, will be exercised by being stretched with the aid of velco strips to create bulk.  All the while the cells are nurtured and grown in growth medium rich with carbohydrates, amino acids and fatty acids.  When mature, the strips can be harvested and then, I guess, grilled! To make a fabulous burger! Hmm-mmm!

If an edible product can be produced from this technique, the implications are huge and can change the way we view meat and food forever.  For example, we can stop feeling guilty  that animals are being slaughtered en masse for our consumption and we will all be obsessed with which university our meat was produced from (Those with a 5-star RAE rating will of course feature in Michelin star restaurants).  However, Post warns that the resulting produce will not be cheap.  He reckons that the resulting burger will cost a whopper £200,000! This cost is justified, what with the great technical skill, the time and labour undertaken to grow and maintain the meat cells.

 One beef burger and one lamb burger in the making...

'Hell yeah!' every cell culture scientist will shout!  For behind the glitzy, dizzying thoughts of solving world hunger and saving all those cute fluffy farm animals (not to mention having a permanent work contract) are the tears and the pure frustration that every cell culture scientist will have experienced in just growing and maintaining those damn cells, nevermind processing them for human consumption!  Mammalian cell culture is a notoriously delicate process: everything from the nutrients in the media to the temperature of the incubator and the level of carbon dioxide present has to be perfect; otherwise, when you look down the microscope all you will see are dead cells floating on by.  There is also the problem of infection, as the cells have no immunity and cannot be made immune: infections from mycoplasma and yeasts, all present in the air or carried on in by the researcher on their skin or clothes, can cause massive cell death of every sample present in that lab.  The infective agent can be difficult to trace and eradicate, and I have seen some researcher friends sigh and shake their heads as their work is being delayed for months as they try to solve this problem.  So sorry sir, but dinner is delayed.  Would you like some lab grown fries while you wait...?

Oh, us poor plebby scientists are donkeys enough - what with be underpaid, unappreciated and unrecognised.  To end up being burger growers and flipper PhD is the ultimate low - and even then the job doesn't get easier!  

An 8oz myco-burger with fries, coming up!  

Source: A Brave New World with Stephen Hawkings


Sunday, 13 November 2011

So it is true, you CAN die of a broken heart!

A phrase normally associated with romantics, poetry and the arts, it can now be revealed that one can actually be heavily - and fatally - affected by one's feelings.  The "nocebo" effect or reaction (Latin meaning "I will harm"), is a medical term used to describe harmful, unpleasant and unwanted effects manifesting in a patient upon receiving a dummy drug.  As discussed by Penny Sarchet in her award winning essay for the Wellcome Trust science writing prize, this is the opposite to the "placebo" effect, whereby upon receiving the fake sugar pill, the patient actually feels better.  According to Sarchet's research these were evident during pharmaceutical trials in the eighties, where heart patients were more likely to suffer side effects from blood-thinning medicines if they had been told of any potential side effects the drugs may have.  The nocebo effect is also contagious; psychological-bourne illnesses have been reported worldwide effecting en-masse, "usually affecting close communities and spreading most rapidly to female individuals who have seen someone else suffering from the condition."

Very little is known about how the nocebo effect works.  A study carried out earlier this year by a group led by Professor Irene Tracey (Oxford) found that when volunteers were subjected to noecbo pain, brain activity corresponding to actual, neurological pain registered on an MRI scanner.  One of the neurochemicals responsible for converting this expectation of pain into a real sensation has been identified by Fabrizio Benedetti (Turin) and colleagues as cholecystokinin, a neuropeptide that acts on CCK receptors that are found throughout the human nervous system.  Cholecystokinin acts on the gastrointestinal system is responsible for bringing about the digestion of fat and protein.  However, it is also causes anxiety and nausea and is administered to test subjects in order to cause artifical panic attacks for research and the development of anti-anxiety drugs.

From these findings Parchet highlights the importance of the doctor-patient relationship.  Since the life and wellbeing of the patient is in the hands of the doctor, trust and confidence in his or her methods are vital.  In light of these findings, if the doctor lacks empathy and social skill or fails to project self confidence, then there is the danger that the patient, fearing the worst, will not respond well to any treatment given to them, as actually verified by Irene Tracey's team.

I would like to expand on that a little.  While not being a researcher in this subject, it is clear that anxiety is rife this modern age and doesn't just exist in medical terms.  It is there as soon as we open our eyes in the morning; it is there as we make our way to work and school; it is there during our entire day and it is there waiting for us when we get home.  From these findings I would say we need to examine our relationships with everyone - if we were all kinder, more tactful and showed greater empathy for eachother, physically, mentally and emtionally we might all be better off. 

Less stress, less anxiety and less heartache.


Wednesday, 10 August 2011

How scientists view each other

It was brought to my attention (by another post doc) that there is a very interesting, insightful and visual of how people in science see each other.  Check this out!

Image taken from DrugMonkey.  Please click to see a bigger image.

I especially like the one where technicians see themselves as Chuck Norris - strolling in and kicking practical science ass - every time and every day! Btw, Chuck can also defend your bench from nifty fingers:

Also check out 'Definitions' to see the "power" status of each member of the lab:

By Lawrence and Gail Bloom 
Appeared in J.I.R., December 1974 


Leaps tall buildings at a single bound 

Is more powerful than a locomotive 

Is faster than a speeding bullet 
Walks on water 
Gives policy to God 


Leaps short buildings at a single bound 

Is more powerful than a switch engine 

Is just as fast as a speeding bullet 
Walks on water if the sea is calm 
Talks with God 


Leaps short buildings with a running start 

Is almost as powerful as a switch engine 

Is faster than a speeding BB 
Walks on water in an indoor swimming pool 
Talks with God if a special request is approved 


Barely clears a quonset hut 

Loses tug of war with locomotive 

Can fire a speeding bullet 
Swims well 
Is occasionally addressed by God 


Makes high marks on wall when trying to leap buildings 

Is run over by locomotive 

Can sometimes handle gun without inflicting self-injury 
Dog paddles 
Talks to animals 


Runs into buildings 
Recognizes locomotive 2 out of 3 times 
Is not issued ammunition 
Can stay afloat with life jacket 
Talks to walls 


Falls over doorsteps when trying to enter building 
Says, “Look at the Choo-Choo.” 
Wets himself with water pistol 
Plays in mud puddles 
Mumbles to himself 


Lifts buildings and walks under them 
Kicks locomotives off the track 
Catches bullets in his teeth and eats them 
Freezes water with a single glance 
Is God …

The eye of Mordor is back tomorrow.  I had better get my get hooves back on the ground and start hauling my load ;-)

'Til then!

Tuesday, 9 August 2011

Back up and running (kind of)

Apologies for my absence, I have been busy.  Things have been a bit heavy at work but they seem to be getting a little bit better.  For several months I have been going through what many scientists go through: frustration, loss in confidence and self doubt.  I had this towards the end of my PhD too, and it is a real killer.  Everything grinds to a halt or is super duper slow, and time and everything else seems to be against you.

It was in these couple of months though that I discovered this blog on Bench Fly.  It has this wonderful section on science and life that contains some insightful and amusing advice on how one's outlook on experiments, life and the like should be.  I am sure there are others like it out there and posts on science forums.

It goes to show that communication with those who have been through it all and having a life outside the lab is essential for dealing with the issues in this line of work.  If you are finding yourself also in a similar situation and everything is getting you down, please talk to someone or join a science forum or read blogs such as the one on Bench Fly.

Most importantly keep healthy and keep smiling.

Thanks for reading x

See: Bench Fly   

Friday, 17 June 2011

Daily challenges in the lab

Ah, such is the life of a scientist, where nothing, nothing is straightforward!  Science never sleeps; it is like a never-ending unfolding story, with as many twists and turns as you like and then some.  Recently, yours truly has been going through a rough patch in the lab of late: a ligation experiment that would allow for some wonderful and intriguing discoveries isn't working, the mutant yeast strains I have generated are not what they seem.  I am repeating some stages in my experiment that I did three months ago.  In the meantime, other experiments I really want to do to get things moving are on hold while I try to find out what I am actually working with.

What the hell are you?! Answer me, damn mutant!!

 If molecular biology was a video game and there were bosses - gigantic monsterous enemies you must battle to get to the next stage (not your supervisor, although opinions may differ on this point) - then ligation would definetly be one big bad boss!  The idea of cutting up pieces of DNA with restriction enzymes and sticking them together with DNA ligase sounds simple enough, but there is a lot of fine tuning involved.  The ratio of vector DNA versus insert DNA is important, get this wrong and it might not work.  The ATP in the ligase buffer needs to be in good condition as this is needed by the enzyme to function.  The temperature needs to be right, the salt and pH conditions need to be right, your mood needs to be right, the funny dance that you do with the pirouette at the end to ward off bad luck...right! 

Giant, evil-looking ligation boss: 1 million points ; tiny, suffering scientist: none

But for now, something is amiss and I need to find out why so I can move on.  One of the frustrating things about science is time: it takes a good few hours to digest the DNA, half an hour to clean it up, half an hour to prepare it for ligation and then another hour for the actual reaction.  It can be so frustrating to find out after all that time it hasn't worked and you have used up loads of enzyme, tons of DNA and it is late in the day so there is little you can do about it - apart from huff and puff all the way home.

So, good people of the blogosphere, if there are any scientists out there who can impart a little advice on how to make ligations work, please feel free to sprinkle me some crumbs of wisdom.  Otherwise just wish me luck - I sure could do with some!   

Tuesday, 7 June 2011

Scientists selling their wares in a time of crisis

Escherichia coli under the microscope (Image by Rocky Mountain Laboratories, NIAID, NIH)

The big news for the best part of a week has been the E. coli outbreak in Northern Germany, and this morning Professor John Oxford, a leading expert in virology and chairman of the Hygiene Council was interviewed by Eamonn Holmes on his views of the outbreak and what advice he could give to the general public to keep themselves safe.

The Professor answered with a brief low-down of where E.coli comes from ( the animal and human gut) how it got from there to the vegetables (animal and sometimes human waste is used to make manure that is used to fertilise crops) and why, in this case, that the E. coli bacteria from the manure has managed to make it into people's mouths (this new mutant strain of E. coli is more "sticky" causing it to stick to the outside of vegetables so that conventional washing is not enough to remove it.  It also has a way of being able to "wriggle" into the vegetable - where no amount of washing has an effect).  All of these points I agree with - the first two points are common knowledge and the E. coli strain (Enterohemorrhagic E.coli ) uses bacterial fimbriae to attach to surfaces, therefore making it sticky.  The "wriggle" bit I am not too sure about as that would suggest the bacteria has a "tail" that would allow for movement.  However, manure is sprayed on to crops and you would imagine that the fertiliser - and the bacteria - is capable of getting into the little crevices and gaps present in the natural shape of the vegetable.

 The shape of the vegetable, the fruit and their leaves makes it harder to remove potential pathogens (Image by User: Geographer)

However, when it came to giving advice on how to keep ourselves safe from getting infected, the Professor seemed to go off subject and talked about personal hygiene, handwashing and how "manners" is important to make sure that others are kept safe from infection by our own actions.  That is all very well and good and I agree one hundred percent - one should wash hands regularly and yes, one should be considerate towards others, like having your hand over your mouth when sneezing or coughing - but how does that relate when it is the foodstuff that is contaminated? How is handwashing and manners going to make the bacteria unstick from your raw vegetables and stop it from entering your stomach?

  If I scrub my hands hard enough, the bacteria from my salad will disappear! (Image by Serenity)

It was the next words that revealed what was behind his statement - I can't remember the exact words but the word "Dettol" was used.  Bear in mind that John Oxford had some involvement in the Dettol Habit survey and that the Hygiene Council is sponsored by Reckitt Benckiser, a multinational corporation that counts Dettol as one of its power brands.  The Professor continued and ended the interview with advice that people should disinfect more.

 The word infomercial comes to mind

It is already bad enough that in cases of disease outbreaks that we, the general public, have little information to go on except that conveyed by the media - information that is usually sensational and serves to promote fear and panick.  Now there are professionals, experts in the field, that are using this hysteria as an opportunity to endorse products and increase their project funding. 

In times of crisis we all look to those with more knowledge and expertise than us to inform and guide us and we hope that their information is in our best interests.  What we don't need is for these people to take advantage of the situation for their own.  What the good Professor should have said is that since the bacteria cannot be easily removed from the raw vegetables or fruits by washing, that they be cooked thoroughly instead before consumption.  This is just common sense and doesn't require a council and doesn't require a study.

It certainly doesn't require product promotion!

Source: Sky news

Also see: Sell it to me!        


Thursday, 26 May 2011

Queen Victoria on film!!!

So there I was, measuring the intensity of the radiation emitting from my southern blot. The click, click, click-click-click sounds from the geiger counter sounded a bit too frequent (meaning that the blot is not as clean as it should be and needs extra washing to get rid of the residue isotope) but that day I was impatient (and a bit desperate!) to see something, anything on my blot. So I carefully dried it on a piece of tissue, wrapped it in cling film, stuck it down in the casette and exposed it to film overnight.

I had expected to see bands on the film of my DNA with some residue blobs here and there. Imagine the shock when I saw this! :

Over-exposure!! At its finest!!!

But look at the outline in the centre. Does it look familiar?

Queen Victoria! On MY film! How cool is that???