Musings of a Me

Not having had much in the way of any real assignments for quite a while now I think that I'd really forgotten how hard I find it to be both concise in my writing yet be scientifically accurate. The object of my current fun is the ~300 word project description for my first placement, which starts on the 1st November. Into this I've got to get the plan of my three month placement, giving enough details to allow the course organisers to ensure they are happy with it before they release the funds. I'd say that it's like writing the abstract for a paper but with no results and more speculation. Added on top of this is that while I have a basic background in the subject it's definitely not as in depth as I'd like so while I'm making headway on the literature it clearly shows that I'm new to the field.

Still, even with this looming over me it's less than a week until I get back into the lab again. All in all the lab work is probably the single part of the course that I've been most looking forward to, though if it wasn't I'd have to seriously question why I was on a PhD programme.

Anyhow, back to the literature before another re-edit of the project description.

There are a number of things in this weeks edition of Nature that I wanted to comment on but I'm a little pressed for time so for the moment here's just one of them, oddly enough from the back of this weeks edition.

First off is the graduate journal that appears on a regular basis and which as a new graduate student I find quite interesting as it provides an idea of the direction my life may take in the next few years. This week the author has commented on a topic that seems to crop up regularly, balancing life in the lab with life outside of the lab, in this case specifically when it comes to relationships. It's a topic that I have to admit has certainly been on my mind the last few weeks as different introductary courses have jumped between the 'expect to have to work hard and do long hours' and the 'make sure you have a life outside of the lab.' This second factor is especially daunting when talking to students coming to the end of their PhD's where they talk of 60 hour weeks or longer when things go wrong. Personally I've always been of the view that while I'm willing to work long hours I wouldn't be happy about making it too regular or doing it week in, week out. The same applies for taking holidays, my supervisor may not be too happy about it but in the end I've got however many days off a year for a reason, to prevent me from burning out and getting sick of the lab. Regular hours and time off will help with that.

Looking at it from another point of view would be to consider the money involved. It's not a topic that I want to mention but generally PhD stipends aren't fantastic and if we were classed as actual workers rather than students then I'm fairly certain that for the amount of hours expected many graduate students would find they fall well below the minimum wage here in the UK.

Then again, much of this is all academic for me at the moment, I'm not in a relationship and I've not actually started my actual PhD.

In the grand scale of things I'm not the biggest fan of science reporting to the general public. Much of this stems from the training I've had to undertake as part of my degree, especially with regards to analysing publications and the data contained within them. So when I see reporting such as this on the BBC I get a little annoyed.

For a start there is very little in the way of actual science in the article, yet it would be easy to see the average person assuming that because the person making the claims is an evolutionary theorist they know what they're talking about. Apparently the logical outcome of sexual selection in a technological human population will eventually create two separate subspecies of humans, one smart, attractive and graceful while the other is dim-witted, ugly and squat. Ok, so this is a possible outcome, but personally I'd say that even over the next thousand years its more likely that there will be events that result in a mixing up of the gene pool again, a prime example of this could well be the collapse of civilisation as we know it. On the other hand the article talks of an increased dependence on technology. Ok so what about genetic engineering? We're already seeing the first steps towards it which ultimately could be used to ensure that everybody is healthy or intelligent hence negating the evolution of a 'sub-class'

Just one final comment which I think emphasises the audience that the report has been aimed for, it was commissioned for the Bravo satellite channel.

Another week gone and yet again I feel like I've not really got much to show for it with regards work. When I started out on my post graduate course I expected to be thrown into work fairly quickly, I guess I wasn't banking on the downtime linked to chosing my first placement, which is due to start in November.

Now though I'm at the point where I'm close to making the first decision on where to go, I've narrowed it down to two laboratories. The first works on trinucleotide repeat diseases which given my background is the sort of field that I expect I'd have gone into if I'd headed straight into a PhD, partially as it's where my limited experience actually lies. The second laboratory works with Epstein Barr Virus tyring to work out the mechanisms it utilises to evade the immune system and how the system can be tipped towards cancer. While it's still broadly speaking got a genetics and molecular biology aspect to it this project is a bit more out of my normal area but still interesting. So now I've got the joy of deciding which to go with and also whether I should approach more supervisors in the time I have before I should decide.

So for now I guess it's back to the joy of journal trawling to try and get a better feel for each of the labs.

Drug development is, by its nature, a very hit and miss process. You may have an idea of the target receptor structure which gives a basis for drug design but beyond that a lot of factors are still chance, especially when you have to consider other targets that the drug may interact with leading to undesired side effects. It's always nice then to see talk of projects such as this one where the aim is to generate a database of drug effects through the use of micro arrays.

Micro arrays are wonderful if expensive pieces of technology as they allow for the activity level of every gene in a given tissue to be examined in one fell swoop. The aim of the project above is to generate a database of this microarray data for various (and eventually all) tissue types following exposure of the cells to existing drugs. By comparison with the same types of cells when the drugs are not present the differences in gene expression can be determined. In itself this is a vast project, further complicated by the problem that the majority of existing micro array data has been generated following different protocols depending on the laboratory and original aim of the data collection. There are also tens of thousands of potential drugs to assess and potentially far more that exist only in the storage vaults of the many pharmaceutical companies around the globe.

In a world where data is becoming increasingly complex techniques such as this are increasingly important for fully analysing the potential of such drugs to determine their full range of use. Additionally by expanding the potential use of each and every drug that a pharmaceutical develops the cost of the research can be covered more quickly, allowing for a reduction in the end price of each product.

So, once again despite my desire to try and get into the habit of writing (yet again) it's been the best part of the month since my last post. Well hopefully that will change now that I'm back in the swing of things by finally starting on my graduate programme at the University of Glasgow, once again bringing me back into contact with science on a day to day basis. In addition its also likely that this blog will end up being the outlet for any of my programme or lab based rants that I expect will occur at some point. I also hope that I'll be able to do some proper reports on the science that I'm interested and involved in, which was the primary aim of this blog when I started it. Given my first year of study is broadly broken down into three placements that in itself should add a bit of variety to the topics. I'll also be looking to make some contributions to some of the carnivals in order to both inform and get in the practise of writing in a more serious style.

A new analysis into the prevalence of the of cystic fibrosis (CF) within European populations has suggested that the mutant gene may be present at its current levels due to it offering protection against tuberculosis (TB), which is believed to have caused ~20% of all European deaths between 1600 and 1900. While two copies of the mutant gene cause full blown CF a single copy may protect against TB with no detrimental effects on the health of the individual.

CF in humans is primarily a disease of the lungs although it also affects a number of other organs including the intestines and skin. Within European populations it is the most common lethal inherited disease and until the latter half of the last century the majority of sufferers died before the age of twenty. Nowadays the disease is more controllable through a combination of physiotherapy, antibiotics and dietary supplements. In the past mutant CFTR, the gene responsible for CF, has been linked to protection against cholera and typhoid as these diseases require the protein that is mutated. In this study however it is suggested that these diseases alone did not, historically, kill enough people to explain the current level of CF in the European populations.

The study then looked at TB and studied its prevalence across the centuries and aimed to correlate this with the presence of CF in the population. Europe has had a long running association with TB and the model that the generated suggests that CF may have reached its current levels if it provided some but not total protection against the disease. Personally I'm not the biggest fan of statistical models, I'm never entirely convinced about the way in which the actual probabilities are generated. This one appears to be relatively simple in generating a correlation between the presence of TB and the frequency of CF. Most reassuringly the model appears to be able to accurately predict the frequency of the CF gene when applied to the Indian subcontinent, where TB has been prevalent for a much shorter time period.

So is this study particularly important in determining a possible link between CF and TB? Honestly I'm not sure it is. In and of itself it is only a statistical analysis and therefore cannot make any prediction as to why having a single copy of the mutant CFTR gene may provide resistance against TB. Personally it is an interesting piece of information that may explain the relatively high frequency of CF in the west. On a personal level the link to CF in itself attracts my attention due to my interest in gene therapy, for which CF is a major focus. For part of my Masters I undertook a lab project in a lab that was working on gene therapy for CF and it is an area of research that I'd like to study once I complete my PhD.

This one's just in from New Scientist Tech where they're reporting on a new scheme that aims to cut the costs for poorer countries with regards the cost of providing textbooks.

The scheme is called Global Text (though at this time I can't actually get the website to load) and is based around the wiki software that is perhaps best known due to wikipedia, a free online encylopedia where the pages can be created and edited by the users. Currently the encyclopedia is available in 11 different languages each of which has upwards of 140,000 articles.

Where Global Text differs is the aim to use the technology to write accurate, up to date, and most importantly free text books covering a range of topics. At the moment the project has set themselves a target of producing (a mere) 1000 textbooks and next year hope to start translation of the textbooks into Spanish, Arabic and Chinese. As any user of wikipedia will know there is always the problem of users who spam, vandalise or even delete pages for a variety of reasons. It was only last year that a high profile complaint was made by a journalist who found they'd been falsely implicated in the Kennedy assassination. Normally it is hoped that other users or administrators will notice errors and falsehoods and either make corrections or restore the page to a previous version. For the most part it works, but then wikipedia has never claimed that it is suitable for anything other than general research.

This though is where Global Text differs, in order to be of any real use the information needs to be as accurate as possible but at the same time must not lock out the ordinary people who are essential for updating the pages. To get around the problem they've come up with a rather nifty solution which just isn't practical for a site such as wikipedia. For each of the textbooks a number of academics with knowledge of the field are given admin responsibilities. Other users are free to contribute and edit pages but until these are approved by one of the admin the changes show up in a different colour, altering users that the information has not been verified.

Whether the scheme manages to get the support that it deserves is something that we'll have to wait and see. Personally I am a large fan of both open source and open access both on and off the web, science is something that should, in my opinion be completely open access and available to all if it is to be used properly. Virtually everybody is familiar with the saying that knowledge is power, giving that knowledge to everybody makes the power accessible to everybody and prevents any single person, group or nation from monopolising the opportunities made available from that knowledge. Within the scientific community open access could potentially reduce the potential for fraud to enter the literature by allowing the data to be made available to all. Nature for example has recently been testing a new model for peer review where articles are available prior to publishing for anybody to pose questions for the authors. While the trial is still underway I hope that the results are positive and lead to the peer review process being made more open in not only Nature but many other journals.

(Once I can actually get the Global Text website to load I'll expand this entry further to give a better opinion of the scheme.)

...is up, over at Epigenetics News with a roundup of some of the best science blogging on the web from the last fortnight.

In other news it seems that the Vatican is gearing up to try and determine a more clear cut opinion on their views on evolution. In itself this is a fairly big development given the influence that the Catholic Church carries throughout the world. In 1996 John Paul II described evolution as "more than a hypothesis" which would appear to put the Vatican on the side of science. Since then however creationism, and the intelligent design aspect of it in particular, has gained much popularity. While the majority of its followers apparently remain with the evangelical churches of the US an increasing (but still small) number of people in Europe are beginning to follow it, including it seems some within the Vatican.

The seminar is due to take place this week, so it is likely that we will know what is said relatively soon. Of maybe possible significance is the opinion of the current Pope, who in his inaugural speech stated that "We are not the accidental product, without meaning, of evolution." While personally the end verdict makes no difference to me I sincerely hope that by this he means that the Vatican is of a view that evolution was directed by God. The alternative is something that I'd rather not have to deal with.

One of these days I'll learn how to use HTML and CSS properly so I can format this blog exactly the way I want it. Until then this will have to be close enough.