Of Science and Handbags

Happy Holidays!!!

2011-12-31T00:48:00.000+00:00

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

Ticked off - and really happy!

2011-12-06T23:20:00.001+00:00

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

2011-12-06T22:09:00.001+00:00

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

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

2011-11-15T20:44:00.001+00:00

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

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

2011-11-13T19:53:00.001+00:00

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.

How scientists view each other

2011-08-10T22:52:00.003+01:00

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:

DEFINITIONS

By Lawrence and Gail Bloom

Appeared in J.I.R., December 1974

CHAIRMAN OF DEPARTMENT

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

PROFESSOR

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

ASSOCIATE PROFESSOR

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

ASSISTANT PROFESSOR

Barely clears a quonset hut

Loses tug of war with locomotive

Can fire a speeding bullet

Swims well

Is occasionally addressed by God

INSTRUCTOR

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

RESEARCH ASSOCIATE

Runs into buildings

Recognizes locomotive 2 out of 3 times

Is not issued ammunition

Can stay afloat with life jacket

Talks to walls

GRADUATE STUDENT

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

TECHNICIAN

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!

Back up and running (kind of)

2011-08-09T22:01:00.002+01:00

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

Daily challenges in the lab

2011-06-17T12:27:00.000+01:00

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!

Scientists selling their wares in a time of crisis

2011-06-07T15:11:00.092+01:00

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!

Queen Victoria on film!!!

2011-05-26T16:49:00.001+01:00

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???

We are human after all

2011-05-16T23:34:00.002+01:00

While trawling the internet, I found this story: 'American biologist trapped on UK beach phones 911... and is rescued after operators in Washington put her through to British police.' Not the finest moment for anyone and especially for one whose profession portrays them to be intelligent and knowledgeable. However, we must remember a job title is just a job title and a qualification is just a qualification. Underneath it all there is a person, who can make silly mistakes just like everyone else. We are human after all.

Lab frustrations!!!

2011-05-11T00:10:00.001+01:00

From practical grievances to writing up and publishing the damn stuff, these links say it all!

Caught in a bad project!

Herr Professor is not amused...

All this leads to everyone submitting their work to this prestigious journal:

Where all submissions, regardless of the quality, will be... rejected! Here are the reasons for why this is a good thing as according to the journal:

1. You can send your manuscript here without suffering waves of anxiety regarding the eventual fate of your submission. You know with 100% certainty that it will not be accepted for publication.

2. There are no page-fees.

3. You may claim to have submitted to the most prestigious journal (judged by acceptance rate).

4. The JofUR is one-of-a-kind. Merely submitting work to it may be considered a badge of honor.

5. You retain complete rights to your work, and are free to resubmit to other journals even before our review process is complete.

6. Decisions are often (though not always) rendered within hours of submission.

Have a nice day and keep smiling!

Check out: Journal of Universal Rejection

I'm cooking on sunshine! (Wooah!)

2011-05-07T20:27:00.000+01:00

The concept of green energy becoming a perceivable substitute for coal and gas was validated again - this time in the kitchen. World-acclaimed Catalan designer Martí Guixé, Finnish food visionary Antto Melasniemi and Lapin Kulta beer have joined forces to present the Lapin Kulta Solar Kitchen Restaurant, where all the cooking is done and powered only by pure solar energy.

According to the official website, the Lapin Kulta Solar Kitchen Restaurant "highlights key contemporary themes: a nature-driven process, flexibility and immediacy. Depending on the sunshine of a given day, the kitchen is able to do a solar barbecue, meals prepared at lower temperatures or salads. The restaurant will therefore also test people’s flexibility: if it rains, we have to adapt, reschedule and deal with the nature-dependent delays. Immediacy will be evident in the urgency of movements and decisions, and real-time information: a cloud could change the course of a business lunch!"

Unlike the traditional way of cooking, solar heat affects the taste and texture of the dish in a surprising and positive way, producing a completely different taste experience

- Antto Melasniemi and Martí Guixé

Last month, their solar cooking project showcased at Milan Design Week 2011. This summer the restaurant will be setting up all over Europe, with the project making a trail towards the never-setting summer sun of the Arctic Circle. Customers can marvel at this creative and innovative use of the sun while enjoying gourmet cooking, beer, life and art.

Check out their website to see if they are coming to a city near you. Once you have found this out and you want to know when they are opening, look up to the sky...

Source: Lapin Kulta Solar Kitchen Restaurant

Biocouture

2011-05-01T01:13:00.011+01:00

How cool is this - Suzanne Lee of Biocouture at Central Saint Martins has established a method to produce material that can be molded into clothing - a method that involves growing bacteria on sweetened green tea in bathtubs!

A biofilm being grown on sweet green tea. Picture courtesy of Biocouture

The bacteria feeds on the sweet tea and grow and aggregate to form biofilms on the surface of the liquid. The cellulose that is being produced by the bacteria (and what holds the biofilm together as a matrix) can be taken after it has grown to a thickness of around 1.5 cm, dried out and molded into clothes. These can be dyed a variety of colours, the quantity of which is needed being less than that for other commercially used materials, an added benefit for the environment.

A Biobiker jacket. Picture courtesy of Biocouture

The Biocouture material is described as having a "vegetable leather" feel. Like vegetable waste when unwanted it can be discarded and treated as compost.

At a time when we are looking for green solutions for various industries, this novel method seems beautifully simple and has a fantastic result. The question remains whether this unique material can be made strong enough for everyday wear-and-tear, can be made water resistant and whether a variety of materials can be made to substitute for the likes of denim or nylon. At present Suzanne Lee, a Technology Entertainment and Design (TED) fellow and her team are planning to scale up this whole process that will hopefully involve the use of waste streams from the food and drink industry. A Stella dress to go with a Mac-mac and a cola clutch bag? I am excited!!! :D

I wish this project the best of luck. I will be looking forward to buying a handbag from them in the not-too distant future! ;)

Source: Biocouture

See also:

Suzanne Lee - a profile
Central Saint Martins College of Art and Design
London Science Museum: Trash Fashion
TED Fellowship

Chernobyl: 25 years on

2011-04-28T02:09:00.011+01:00

A sarcophagus in the Chernobyl Zone. Image by Piotr Andryszczak

26th of April was the 25th anniversary of the Chernobyl disaster. The Presidents of Russia and Ukraine attended a commemoration ceremony at the site of the world's worst nuclear disaster and were united in calls for new international ruling to ensure the safe running and development of nuclear facilities.

The explosion and fire at the Chernobyl facility based in the former USSR released massive quantities of radioactive material into the surrounding area and into the atmosphere, where it was detected as far away as Norway and Scandinavia. To this day, the areas most effected by the nuclear fallout are still dealing with its aftermath - large areas of Belarus, Ukraine and Russia are still contaminated with heavy radioactive elements. Death and poor health attributed to high radiation exposure are still being reported.

Chernobyl radiation map from CIA handbook

President Dmitry Medvedev did not specify what proposals he would bring to the international community. He did, however, stress that the Chernobyl disaster has taught that truth and honesty is paramount to protecting lives: "it is duty of the state to tell the truth to its people. It must be acknowledged that the (Soviet) state did not always behave correctly".

However, lessons from the present-day disaster at the Fukushima nuclear plant must also be recognised. Here, the incident was not a man-made accident like Chernobyl but caused by the uncontrollable and unanticipated force of nature. To save lives, one needs to know at an instant the extent and the immediate consequences of the damage to the facility and the impending nuclear fallout in order to take effective action - knowledge that could not have been apprehended fast enough for the officials in Japan to make any formal statements. It is here that honesty and truthfulness, under a massive plume of radioactive dust, do not appear to hold much value.

A word that does appear to be of value is conscience. What we know from both these major incidents is the sheer magnitude of the danger that a nuclear fallout poses to life and health; a danger that cannot be naturally sensed or outrun, that can be so easily caused by man or nature and that is irreversible, destructive and long lasting. One must question whether our demand for energy outweighs the value of human life and the value of our environment - one that in future will be serving as a massive dumping ground for nuclear waste.

Safer, renewable and clean energy technology exists. Now would be the perfect time for world leaders to listen to their conscience, and their people, and make a move away from the tempting toxicity that is nuclear power. What should be the real take-home message from Chernobyl and Fukushima is: haven't we seen enough?

Source: Reuters

Also see:

Channel 4 4od: Nuclear Eternity

Heavy Water: A film for Chernobyl

RNase Evil

2011-04-27T00:52:00.005+01:00

For those scientists working with RNA you will feel my pain: so I got in early today to set up an RNA glyoxal gel:

I loaded my RNA samples, ran the gel for 5 hours and this was the result:

Arrraagh!!!!!!

It appears that I have RNase contamination in my gel! This is an enzyme found in abundance on skin (and in saliva and tears) that specifically destroy RNA, hence the horrible smeary bands you see. RNase can be found on almost every surface in physical contact and is hell to get rid of. For a better description - and for how I and many others who work with RNA feel about this enzyme - check out this page or just take me at my word - Evil! Evil! Evil!

Imagine you are the RNA, and those are RNases...coming after you...

RNA stands for ribonucleic acid and is one of three types of macromolecule (the other two being DNA and protein) that are essential for all forms of life. RNA is very similar to DNA in that it is made up of a string of nucleotides, the sequence of which allows RNA to encode genetic information, similar and as derived from DNA. However, unlike DNA, different types of RNA molecule exist, and are involved in many enzymatic processes within the living cell: that as well as encoding and passing on the information to synthesise proteins, RNA can direct and regulate gene expression, function in protein synthesis and sense and respond to cellular signals.

An x-ray structure of transfer RNA - a type of RNA that is involved in recruiting and linking amino acids together in the process of protein synethesis. Image by Yikrazuul.

Yet despite being so deeply involved in many vital biological processes RNA is very unstable. This is not surprising since a lot of these processes are rapidly occurring and are responsive to internal and external factors. RNA molecules generated now may not appropriate for what may occur at a later stage; their prolonged presence may even be deterimental to the cell in that specific catalytic processes may be overexpressed or suppressed; certain functions may be deregulated. One can say instead of being cogs in a well oiled machine they are now like spanners in the works.

So, yes, it is good that RNA is easily degradable and RNase is in abundance to do it - just not when one is trying to isolate and study it!!! So it will be take-two tomorrow: I am going to encase my hands in chain-mail gloves and treat all my equipment and my bench with a flame thrower. Hasta la vista RNase...

Kidding!!!

Wish me luck!

Of Science and Religion

2011-04-25T14:01:00.004+01:00

Depiction of Jesus Christ on stained glass. Image by Toby Hudson

While enjoying the Easter holidays I came across this article in the New Statesman where the author, Andrew Zak Williams, interviewed a variety of leading public figures and scientists on their views on Christian faith and their reasons for believing. The responses are diverse as they are fascinating - Religious leaders James Jones and Richard Chartres describe the Christian faith as unquestionable. Others such as the barrister Cherie Blair, journalist Jeremy Vine and former Conservative minister Jonathan Aitken see religion as natural and a form of solace, something that cannot be explained. The British author Peter Hitchens and Professor of Psychology David Myers find that faith provides a guide and a meaning to life, that it holds the key to the many questions of the universe and of our existence.

It is perceived that the scientist's view is a little more divorced than those expressed and in this article it shows - Quantum Physicist Paul Davies prefers "useful concepts" than belief; that the word 'God' is undefined and idea of a spiritual entity capable of thought and control is unacceptable. Theoretical physicist Peter Richmond goes further, stating that although the teachings of the Bible are still relevant to this day, the scriptures should not be taken literally. However, the likes of Professor of biology Kenneth Miller, astrophysicist Hugh Ross and Professor of climate change Mike Hulme confirm a personal belief in the Bible and in God; a belief that stems from, surprisingly, scientific findings, scientific rationality and scientific values.

There is a concept perpetuated in the UK media that science is very much against religion - that it is God versus Nature; creationism versus evolution. However, from these short interviews it can be seen that the lines are blurred - that there are well respected and successful scientists who openly embrace religion and the concept that scientific methodology is not appropriate to explain or define faith.

Source: New Statesman

Happy Halloween - I mean Easter!

2011-04-17T02:24:00.017+01:00

Lets go easter egg hunting!! Image by Paul Sapiano

It is past midnight and I am desperately fumbling for the remote control with my eyes closed to get rid of the creepy advert of yet another horror movie from my TV screen. It's April, for goodness sake! Easter is but a week away, our Kate and Will's wedding is not far off either; it should a time of sunshine, celebration and scoffing Easter eggs. But no, instead, some of us will be happily heading on down to the cinema to take a proverbial dump in the pants:

Why??????

An article blog by Norman Holland (Psychology Today: Why are there horror movies?) suggests that one can find satisfaction from experiencing fear and other unpleasant emotions. As living beings, we learn from a whole host of sensory cues. Fear and other negative emotions signals for danger and from an evolutionary stand point it does us good to pay attention and learn from the situation in order to help us survive. As human beings we enjoy learning, therefore maybe we enjoy learning the art of survival through fictitious media. However, Holland suggests that it is all down to the economising of psychic energy: in an unreal situation we have no need to respond to what is happening. We can just watch and learn and go with the flow and this (apparently) can be relaxing and quite satisfying. In reality however we would be more inclined to do something, like call the police or go knock out that p***k with the mask on. This requires brain activity, extra energy and with the addition of the impending adrenaline rush that energises the fight or flight response, it is this that causes unpleasant sensations.

So having learnt all that, how come I (and others) are such scaredy cats?? I can say in my case I maybe have more of an emotional response to what I perceive, whether it is real or not, since I feel really depressed when I watch sad movies and laugh out loud at comedies. One of the appealing natures of any storyline is that it draws you in to feel for the characters, and that's a good thing as otherwise it would be really boring! However, for the more emotionally sensitive amongst us, movies, books or games invoking negative emotions is a big no-no. I'll go and hide back behind the sofa now...

Source: Psychology today

See also: Norman Holland - Marston-Milbauer Eminent Scholar Emeritus

New bag!

2011-04-16T21:05:00.019+01:00

Alas, commuting has taken it's toll on my wheelie bag. For a week or two I had started noticing that my laptop case was looking a bit dusty. I just thought it was my DIY lining on the inside of my wheelie bag coming off. Turns out there was a huge hole at the bottom of the bag near one of the wheels. I had been dragging my laptop along the floor all this time!!!!!!!!

I have since gotten a new one and it is no way as good as what I had - the compartments are too small, I have to put my lunchbox in sidewards, and I can't haul shopping in it either. The upside is that it is designed to hold a laptop so it is all protected, and the wheels are a bit bigger.

Maybe I should ditch it and go more high-tech - there are now bags you can get with solar panels that can generate energy to charge up your laptop (check out Voltaic):

Pretty cool no? Now if only it had wheels and I could haul shopping with it that would be great!

Sell it to me

2011-04-11T22:43:00.007+01:00

Hmmm, I'd like a coffee please! (Image by Marshall Astor)

Having worked in molecular biology research for 9 years and still counting, I can conclude that being in science is very much like running a business: the Principle Investigator (the P.I., the boss) is like a sole trader; their laboratories are their work premises; they employ students, technicians and post-doctoral researchers who are all paid with monies obtained through research grants; their heavy-duty equipment (also obtained through grants) is their capital; stock consists of glassware, disposal containers, pipettes, bins, chemicals, growth media and the like. There are bills to pay, health and safety regulations to adhere to and obligations to fulfill, such as teaching and lecturing. The major object of trade is data.

To be successful in academic science one has to be successful in the business of generating data. And not just any old data - positive data, exciting data, data that tells a story. Data that gets everyone in your field of work talking. Data that scoops anyone else working on your topic. With funds becoming scarce and more complex to obtain (see blog entry: Fat cats and dead rats), it is now necessary for scientists to have not just good communications skills but good selling skills too. Depending on the interest of the charity/trust who acts as the bank, a research proposal needs to be written in a way that it can fulfill that interest - even if it may never happen. This seems dishonest, however as mentioned in my last blog a lot of science is developmental. Like the initial design sketchings before a form takes place, the nature of scientific research is full of uncertainty. But it does allow questions to be answered, more questions to be asked and doors to be opened to many different possibilities.

There are various ways a scientist can sell his wares. Most communications in academic science occur not only through relevant scientific journals but through conferences and meetings held by the relevant societies. The more popular the topic (i.e. those of public interest such as the environment, food, health and energy) the more a scientist has access to popular medium, such as newspapers, science magazines, radio and TV. It is here in the bright lights that the information being conveyed gets confusing. With many seemingly expert opinions, it is hard to make sense of it all.

A good example of this is the ongoing claims about the health benefits and risks of coffee . In 1999 it was claimed that coffee drinkers are less likely to suffer heart disease compared to those drinking tea (BBC News Health). But then in the same year it was reported that too much coffee leads to elevated stress levels and increased blood pressure (BBC News Health). In 2004, the story changed again with an Italian dietian stating that coffee has a whole host of health benefits - "the stronger the better" (BBC News - again). But don't drink it cold - in 2009 it was reported that iced coffees bought from the high street may increase the likelihood of obesity and cancer (Sky News). Not for Prince Charles though - he was reported to back a controversial therapy involving coffee that could cure cancer (The Guardian). The coffee, however, will not be for drinking purposes.

Some communications in popular medium appear more like hard sell tactics, arising from situations in current events. A recent article in The Guardian pulls out all the stops to confirm that nuclear power has greater benefits than the risks perceived. Another article in the The Telegraph states that even small amounts of alcohol can lead to the risk of developing certain types of cancers. Here, one is more likely to question the reasons behind this: a face-saving tactic by the representatives of the nuclear power industry perhaps? A way to reduce National Health Service bills of treating alcohol related incidents/diseases?

Only those in the know can truly say how the science is being sold. In any case, one has to be quizzical of the information being conveyed, even if it is being backed by scientists and experts.

Enjoy your coffee.

Fat cats and dead rats

2011-04-04T23:45:00.017+01:00

Image by brokinhrt2

Today I went to the first of a two day course titled 'Career Management for Researchers - Broadening Horizons'. The aim of the course is to recognise that with so few academic positions available nationwide, it is necessary for university staff on contract employment (such as yours truly) to think about the transferrable skills we have in order to find permanent employment elsewhere.

The declining number of positions is in line with the cuts the UK government has announced for university funding: according to The Guardian £940m will be cut from the 2012 budget for teaching, research and buildings. This announcement is a massive blow for science departments everywhere who are already struggling to obtain funding. The regulations to date, set by various research councils, state that successful research proposals should have a social or/and economical impact. This has put a huge pressure on laboratories, such as the ones I have worked for, that carry out what I call 'pure' research; where a subject is being studied solely for the expansion of knowledge and discovery. The findings of these projects are by no means "useless" or a "waste of money". It is the probing nature of this type of research that leads to the better understanding of the complexity of life, in the standpoint of physics, chemistry and biology. I believe that forced cessation of such projects will lead to the decline of useful knowledge that could lead to the discovery and development of new medicines and technology; the vital component of work that, ironically, would have a social and economical impact.

The announced cuts for 2012 means that many research groups will be scaling down and tightening belts than ever before. Many highly qualified and talented individuals who have trained long and hard and have made many personal sacrifices for the sake of their careers will be unceremoniously made redundant. This is insult to injury since professionals in other fields of work have excellent job security, decent pay and benefits and, most importantly, are recognised and appreciated.

Tonight, as I wring my hands at the prospect of being a job seeker that is too old and too over-qualified for most types of work, I see that our Vice-Chancellors are not feeling as worried. Dispatches on Channel 4 has reported that while universities are facing cuts, students (their parents) will be hit with massive tuition debts and academics and researchers will be out of a job, university Vice-Chancellors are livin da vida loca with salaries up and over a quarter of a million pounds. In addition, they reside in luxurious accomodation and have ski chalets, chauffeured driven cars, membership of exclusive clubs - all taken care of by the "cash-strapped" universities. My hands are wringing even harder.

Memories of a quip from an ex-colleague enters my mind: "it is time to find a real job". This epitomises the life of a present-day academic science researcher. Far from the romantic ideal that universities are a haven for those who wish to make a living through knowledge and discovery, the reality of the situation now is that through commercialisation the fat cats are getting fatter and the lab rats are facing certain death.

See: Dispatches

No thank you, GM cows...

2011-04-03T02:31:00.029+01:00

It was reported late yesterday evening that researchers at the State Key Laboratories for AgroBiotechnology in China's Agricultural University has successfully introduced human genes into a herd of cows in order for them to produce milk similar to that of human breast milk (see The Telegraph). This latest advancement in GM research is to enhance the presence of key nutrients, missing or found as a low level in cows milk, that are vital to a baby's health and development. At present, three types of genes have been incorporated by microinjection of the modified genetic material into bovine somatic ('body') cells. The nuclei of these cells were then transferred into donor cells, from which transgenic bovine embryos were created and the resulting cows could express lactoferrin, lysozyme and Alpha-lactalbumin in their milk. The observed high yields from these "mammary bioreactors" is seen as a positive step towards the industrial scale production of GM milk.

The process of creating clones by somatic nuclear transfer (taken from de: Quelle: Zeichner: Schorschski / Dr. Jürgen Groth)

However, these findings will also alarm and outrage those who are against the use of GM for food production. There is the obvious safety issue of consuming products that have been unnaturally enhanced and of which the short and long-term effects of consumption are unknown. There is also the concern for the welfare of the animal, since the previously created Dolly the Sheep - although deemed a healthy clone - had an unusually short life-span and suffered health problems.

In the UK, the concept of GM food has had so much bad press that supermarkets go to great lengths to stress that the food they sell are GM free. Furthermore, the use of breast milk for commercial purposes has already caused quite a stir - the recent offering of "Baby Gaga" - breast milk ice cream made from donations of a lactating mother - has invoked mixed feelings ranging from curiosity to disgust (see BBC News).

The question that weighs heavy on my mind is this - why is it that these cows are required when a human mother is quite perfectly able to feed her own child? For argument's sake, there are those mothers who are unable to feed their baby, such as those with a medical condition or are taking/addicted to substances that could risk harm to the baby. However, cannot a human lactating mother donate milk for this purpose? In the case of the ice cream, there were a number of mothers who expressed an interest in offering their milk for financial gain. Cannot healthcare companies/the government pay these ladies to help fellow mothers in need?

In the commercial sense I suspect that when the time comes, the marketing ploy to convince western mothers to use GM milk will be largely based on cosmetics. The perceived unattractiveness of "saggy boobs" as a result of 6 or so months of breastfeeding per baby could be totally avoided by the use of an alternative and equally nutritious source. If that is the case, vanity has reached new heights.

In conclusion, my personal opinion is this - Mothers and women of the UK should unite, burn those bras and chain themselves to the gates of parliament in protest. Not only is breastfeeding a way to feed a child it is also crucial for the bonding between mother and baby; the first step towards building a relationship that is positive, unique and special. Scientific commercialism, vanity and social pressure should not be allowed to undermine its importance. No thank you, GM cows.

Story: The Telegraph

Also see:

PloS One

Wonders of the Universe

2011-04-02T16:44:00.009+01:00

After being awed by the sight of the supermoon (19th of March of this year) and oohing and aahing at the revelations by Professor Brian Cox in his aptly named TV series 'Wonders of the Universe' (its over now, making Sunday evening TV boring again), I started trawling the internet for more fascinating and inspiring information on the cosmos (that is easily accessible and understandable to non-physics-or-math-geniuses). Here is a really great page I found: apod is updated daily with pictures taken by NASA and various other sources and features commentary by professional astronomers. These guys also have a lot of fun it seems! Enjoy! :D

Check out:

Supermoon pics

BBC - Wonders of the Universe by Prof. Brian Cox

apod

Bags on wheels!

2011-04-02T00:26:00.003+01:00

Bags, bags, bags. Everyone knows how much a girl loves bags. I got two that I take to and from work. The second one isn't by choice really. When I started my job the boss told me that they didn't have any office computers. In fact they didn't have anything so I had to bring my own pens, pencils, note pads, tape, gluestick, staples, paper-rock-scissors and get a laptop - fast. The cheapest laptop had all the basic specs I needed but weighs a ton. As I wasn't going to leave my purchase in a place frequented by opportunist drug addicts I needed a mode of transport for my laptop that allows me to keep my posture, muscle tendons and good temperment intact while lugging it to and from work. So all hail the wheelie bag! The saviour of commuting souls. The all faithful container of workstuff, lunch and other personal items. The epitome of convenience. I can't harp on about it enough!

Necessity is the mother of all innovation. I don't know much on the history of the bag or the wheel so I will say this: I love the guy/girl who invented the wheel! I love the girl (it has to be) who invented the bag! I love my wheelie bag! :D

What I would look like if my bag didn't have wheels (image by Thiago Piccoli)

It's all Chinese to me...

2011-04-01T01:27:00.006+01:00

And in a few years time it might be. Recently the UK's national academy of science, The Royal Society, carried out a major study on the global scientific effort (Knowledge, Networks and Nations). The study notes the "striking" rise of Chinese science in terms of the number of scientific findings being published in recognised international scientific journals. At the time of the study, the number of publications orginating from the PRC stood at 184,080. This is a significant increase from the 25,474 papers being published in 1996. Compare this to the number of publications originating from the United States, the country that at present is number one in all areas of science. Here, 316,317 papers were published at the time of the study; a slight increase from the 292,513 papers being published in 1996. The study by the Royal Society suggests that after 2013 the PRC may overtake the US as the leading country in scientific research. The rise of scientific progress in India and Brazil, and the emergence of science in the Middle East, South Asia, North Africa and some smaller European nations also indicates a shift in the global scientific landscape where the likes of the US, Japan and Western Europe have been dominant.

So how did this change come about? As indicated in the study by the Royal Society the increase in collaboration between scientific communities has extended beyond international borders. The common interest of a particular field and the pursuit of a common goal has allowed the forming of specialised organisations and societies that convene on a regular basis to discuss and challenge ideas and to share knowledge and expertise. I myself have been to one such meeting (organised by the RNA Society in Berlin, 2008) and found the experience awesome, insightful and thought provoking. It is at these meetings that scientific collaborations are born, where ideas and solutions originate from a figure on a poster or the from the presentation and words a very nervous speaker (they don't call us labrats for nothing!). Furthermore, with international travel becoming the norm more and more scientists are taking the opportunity and travelling greater distances to present their work to a wider audience, to study and gain experience from a different lab or even moving and settling in a different location altogether; taking advantage of the expertise and technology available. A great number of scientific publications now contain the names of researchers from more than one institution.

So why in the PRC? The economy of the People's Republic of China is the second biggest in the world after the United States. It is also the world's fastest growing economy and one that emerged unscathed from the global recession that has had major effects on the US, the UK and Japan. The wealth and affluence in this emerging super power is attracting the interest of many scientific laboratories around the world. To be able to obtain financial backing is crucial to the life span of a research project. The PRC has the funds and wants in return the knowledge and know-how to further develope its own scientific base, in the form of institutes, technology centres and researchers.

The Royal Society recommends from the study that the support of international science should be maintained and strengthened and that international collbaoration be encouraged, supported and facilitated. This is true since it is scientific research and discovery, not nationalism, that is paramount for preserving the true quest for knowledge.

Having said that though, it wouldn't hurt to start learning some Chinese...

Story: Knowledge, Networks and Nations