Wednesday, 9 November 2011

tMoL: Big Cell, Little Cell

I’m writing this as a homage to one of my closest friends on the blogosphere. The every wonderful LabRat has finally ended her fraught relationship with scientific research and is throwing herself wholeheartedly into science writing. Whilst I am hugely envious, I wish her all the best and hope she will remember me when she is rich and famous. Look out for her in future publications.
By way of background; Lab Rat has always had a fixation with the simpler things in life, by which I mean bacteria.

False colour E. coli, bacterial/prokaryotic cells.
All living organisms are made up of cells individual living units which are relatively self-supporting and capable of total self-replication, although this is complicated by the intricate interactions between different cells in larger organisms. Whilst larger creatures, like humans are made up of billions of cells, the vast majority of life on Earth exists as single celled microorganisms that cannot be observed with the naked eye.
Cells fall into two main groups, larger and more complex organisms, plants, animals and fungi are called eukaryotes (that’s us humans too) and have much more intricate cellular structures. The earliest forms of life, with the simplest cells are called prokaryotes, which include bacteria.

Monday, 31 October 2011

Resurrection: Halloween, spooky proteins and the return of ClearSci

It’s Halloween night and a dark shape is moving towards you through the ether of the information superhighway. Surrounded by the blackness you feel something closing in, disturbing the thick layers of accumulated dust. Just as you’re about to start screaming in terror… IT’S ME!!! Lights on, and by gosh it’s a mess in here, I don’t remember putting all of these spiders up for Halloween. Eww! Eww, eww, they’re real. I’m really going to need to spend some time cleaning all of this up…I’ll deal with that later.

Halloween revival.
So, if you’re here that means you’ve been on the look-out for more of my slightly eclectic and sporadic brand of science writing and I will try not to disappoint this time. Just so we’re all caught up, no I’m not dead and neither is this blog, it just went into reverse-hibernation over the summer (that’s called aestivation, if you’re interested). Also, neither of us has been temporarily reanimated for Halloween, this will hopefully be working its way back into my normal routine.

Summer was great! Although crazy, so I didn’t have much writing time (poor excuse I know). I joined the college graduate committee so I’ve spent a lot of time planning and organising events for our new freshers and negotiating college politics. I also finished the third rotation for my first year (currently in editing for the Wellcome Trust), selected my PhD project and wrote the full project proposal (I’m back with the second lab, playing with fission yeast genes). All of that earned me an MPhil which I will be collecting sometime in the new year.

Monday, 16 May 2011

Sci Comm: The Next Generation

Hi everyone! As always it's been a while. Sorry. There's been a lot of conferences lately and I'm currently house hunting, which means this place and my PhD have both been feeling a little neglected. First I'd like to congratulate NASA for another successful shuttle launch today and second, I have an exciting new post for you.

This is all about a one day conference that was held here in Cambridge last Wednesday for a select group of people from sicence media, predominantly including journalists and film makers, all of whom have extensive and well developed online personas. Several of us from BlueSci where very honored to be asked to attend too, as the focus was squarely on the future. Where we at BlueSci, as aspiring science writers could take the field in the coming years.

The day was full of exciting and controversial bits of debate and we got to hear lots from many different view points about what science journalists should be doing and how we should be interacting with academics and the public. Here I have outlined the major topics discussed, more details are available elsewhere (see the end). Whilst I dod find some opinions difficult to agree with, it was interesting to hear what everyone had to say and I feel I have gained a lot from the experience.

Also I'll hopefully be posting again soon as following this conference I saw Simon Singh again, along with Ben Goldacre and Brian Cox on their Uncaged Monkeys tour here in Cambridge, so stay tuned for that.

The crest of Jesus College
What is the future of science media and science journalism in the 21st century with all of this new media and the shift of communications onto the Internet? This was the focus of a one-day conference hosted by John Cornwell at Jesus College, Cambridge.
The day took the form of a series of open discussions with two leaders providing focus to the discussion. After a warm welcome by John Cornwell, John Naughton opened the first session by discussing the opportunities and challenges involved in adopting new media. He focused on how newspapers have become news organisations, with the paper being one of many media products. Science journalism was effectively compared to a developing ecology where a few large dinosaurs are being replaced by a myriad army of journalistic, blogging termites with a corresponding increase in productivity. The reduction is media size was also highlighted; people buy tracks not albums, read stories not papers and posts not blogs. He asked the questions: How do we add value to a story amidst such competition? And who pays for good journalism when so much of it is free online?

Tuesday, 3 May 2011

A Right Royal Easter Spring Conference

Hi everyone! Sorry for the neglect, I'm working on several things at the moment so this place has been a bit neglected (hides the cracks in the paintwork). Have no fear that I do have several things chasing each other round my brain and one or the other of them may actually make it into print shortly.

Firstly, the launch of the Easter issue of BlueSci is expected on Thursday, so it's been crazy getting that printed and making sure that the online version will be ready to go too. Thankfully I think I'm on top of that now, but that was quite a few evenings eaten.

Also, and probably most excitingly, I went to my first real, proper, grown-up conference over most of last week so what with the long hours I was a bit short on news hunting/writing time. I did however squeeze in time to write several daily pieces for ConferenceCast, which will be appearing over the next few days. It was really cool, focusing on Cell & Developmental biology so we had loads of great speakers (and the occasional dull one, but not everyone's perfect). The prize winners were all awesome and really interesting, especially the Beddington medal winning PhD student who used music to illustrate how well cells moved together during migration.

Now I finally get some time in my third and final lab of the year, 2 weeks after we offcially started, so it's going to be pretty intensive to try and get some results in just 7 weeks. Also I'm putting together a poster about the importance of science communication for a one day conference later in the week.

 I also had to watch the new series of Doctor Who, of course, which is fantastic, although like everyone else I have NO clue what's going on.

So if you've been missing my senseless ramblings you can pop over to ConferenceCast and see exactly what I've been up to and I promise to get my next proper piece up ASAP and to stop writing all about myself.

Wednesday, 20 April 2011

Me, myself and I

This is kind of a long update, but it covers everything I've been promising to tell you about since Christmas. Hope it's interesting, it's certainly been fun for me.

So, last term ended up being slightly busier than I’d planned. The science communication stuff has been going really well, I’ve been writing and editing, I did a bunch of talks and co-organised an unconference called SciBarCamb. Then there was the lab work and review essay as part of the PhD course. Plus, naturally, I had to get some baking in there and the intermediate massage course. Hopefully a bit more breathing space in the last term of the year.

Screening cake based on images from my project.

Full details of last terms project will be up shortly and will also be appearing on the Wellcome Trust blog as the next in my series for them describing my rotations. It’s been a lot of fun and I really enjoyed working with the lab, they are also very responsive to bribery by cake, which was very useful for me. That’s what resulted in screening cake. A set of cakes based on images from the yeast genomic screen we’ve been doing.

Sunday, 10 April 2011

SOS: Save our Science - Stem Cell Abuse: Taking Advantage

So I'm feeling reenergised after SciBarCamb yesterday, very successful, more details to come. I've been storing a few posts up on my hard drive so I probably should get round to posting a few before the new term starts. Heres the first then, the results of an analysis of dubious 'stem cell treatments' which are taking advantage of the general public. Find out what is being done and how to protect yourself. Thanks for this one go to severa of my friends here in Cambridge who are big stem cell fans.

Stem cell technology has rapidly become one of the most well known recent advances in the biological sciences. They have excited many with the promise of cures for innumerable, common and debilitating diseases which affect millions worldwide. Stem cells have given hope to the hopeless, yet many are now taking advantage of this desperate hope for their own gain. False treatments are now everywhere, praying on severely ill patients and their families, with overblown promises of miracle recoveries and jargon-filled pseudoscientific literature which seem to support these sham therapies. These methods are often based upon obscure theories, which are not supported by proven, open, peer-reviewed evidence. This current situation not only threatens the patients who submit to these schemes, but is likely to significantly hamper advancement of legitimate research and the development of real, effective cures.

Cells being extracted from the early embryo for stem cell production (source)
The International Society for Stem Cell Research (ISSCR), concerned by the current lack of safeguards on stem cell treatments, has produced a report highlighting the problem and discussing tools that they are developing to help protect the public and keep everyone aware of which stem cell technologies have been scientifically proven to be safe and beneficial. The online resource, to be provided by the ISSCR, will cover three main points: A list of safe clinics etc. which meet standards of efficacy and safety, information for patients and families on the science behind stem cell research and its clinical applications, and a list of questions that should always be asked before consenting to treatments.
The report points out that many of these stem cell therapies charge patients extortionate amounts of money, this is unusual for any experimental therapy, which will usually be financially backed by government, research or commercial groups, interested in the safe and ethical development of new medical approaches. This is a key indicator of an unsupported scheme which could carry many potential hidden dangers. The ISSCR also recognises that, in order to address this problem, it requires the support of other organisations, including governments and scientific regulatory bodies.

New guidelines and resources are being established by the ISSCR (source)
 The ISSCR has already done much to establish guidelines and regulations regarding stem cell research, and has produced guidelines for the correct methods that should be followed when developing and clinically testing new stem cell technologies. They have decided that stem cell development should follow established clinical trails guidelines, similar to those used for most new drugs and surgical approaches, subject to constant ethical and scientific appraisal and review.

A lack of openness and unwillingness to share data and methodology is characteristic of questionable treatments that are best avoided. If a group is unwilling to discuss with others how it gained its results then they probably have something to hide. As such their findings, and claims, are probably scientifically unsound. This has all been clearly and precisely defined as a set of guidelines by the ISSCR, which stem cell studies should conform to in order to be considered scientifically valid and ethically safe.

The ISSCR task force has outlined, in detail, the process that it will follow to identify clinics offering stem cell treatments and to contact them and investigate the validity of their research. Their findings will be published for use by patients considering treatments, and will allow submission of new clinics for investigation. This resource would also be fully referenced and up-to-date, allowing further investigation of any group listed and ensuring information is always useful and relevant.

Embryonic stem cells in culture (source)
What I find most exciting about this report is the focus on public awareness, something that is often sorely lacking in research fields, particularly ones that have previously been treated with such hostility, as stem cell research has. The paper closes by highlighting the importance of presenting these finding publicly and involving journalistic media, not just the normal scientific publication routes. Is the scientific establishment finally realising that it needs to get the word out to the people in order to advance?

The ISSCR has committed to “avoid overstating what is currently known, whether in the scientific domain, the clinical domain, or the commercial domain” and is working hard to ensure that the entire scientific community conforms to this promise. However, a lot of work is needed to implement all this, and questionable stem cell treatments are on the increase. For now, be cautious, whilst stem cell research is something to be supported and it holds a lot of potential, it is important to avoid being drawn into scams which are likely to leave patients even worse off than they already are.

Taylor, P., Barker, R., Blume, K., Cattaneo, E., Colman, A., Deng, H., Edgar, H., Fox, I., Gerstle, C., Goldstein, L., High, K., Lyall, A., Parkman, R., Pitossi, F., Prentice, E., Rooke, H., Sipp, D., Srivastava, A., Stayn, S., Steinberg, G., Wagers, A., & Weissman, I. (2010). Patients Beware: Commercialized Stem Cell Treatments on the Web Cell Stem Cell, 7 (1), 43-49 DOI: 10.1016/j.stem.2010.06.001

Friday, 25 March 2011

tMoL: Genotype vs. Phenotype

It's the end of another term, time for me to move on again. I'll be going home soon to write about what's been going on, and there's a lot to say. The talks I did in schools went really well, although there's still stuff to improve on. This lab placement has been really great and I've been enjoying all the other projects I'm involved in. Next up is an unconference, SciBarCamb, which I strongly recommend to anyone reading this blog.

This is a peice I wrote for a friend of a friend, she's doing a course in genetics and was looking for clarification of the difference between genotype and phenotype, it was a bit of a rush job but hopefully it clarifies matters.

In order to live, grow and make more of themselves, cells need to have instructions. These are stored as DNA, which is mostly found in the cell nucleus. Each set of instructions is called a gene, each gene produces a particular protein. The full set of human DNA, the human genome, can make thousands of proteins and each protein performs a specific function within a cell.

Genes are specific DNA sequences (source)
 Different people have different versions of the same gene and hence of the same protein, this is what makes us genetically different. These different gene alleles have different effects within our body. As a simplified example; there is a protein which is responsible for hair colour. If it is functioning properly then you have brown hair. Some versions of the protein do not function properly so there is no colour made, this results in blonde hair. There are various other versions with intermediate effects resulting in all different hair colours. This is a slight simplification, as there are actually multiple proteins involved in hair colour, but it illustrates the principle.

Friday, 11 March 2011

SOS: Save our Science - Yet More Alien Bacteria. Really!

I saw James Watson last night! and I have his autograph. :D He was in London, in conversation with Brenda Maddox, who wrote Rosalind Franklin's biography. It was fascinating, although I have to admit that he was clearly on his very best behaviour and kept the outrageous comments to a minimum. I'd also like to take this as my excuse for any 'enthusiastic' comments in the post below, which is a great peiece of storytelling. This week was also my first outreach talk to school children, I think it went rather well, although I'll be writing much more on that in a few weeks.
OK, so this is another story that I was asked to write (Yay!). Once again there have been reports of alien bacteria in meteorites (that’s the third time in 14 years, if you’re counting).Here is the latest story, I suggest you read it first as it makes what I’ll be saying more surprising. Go on, I’ll wait. Sounds good doesn’t it, highly acclaimed doctor with a paper in a prestigious sounding journal, with authoritative quotes and everything. Not only that but the journal seems to have gone to great lengths to ensure extensive peer reviewing of the findings before publishing. Well, as with many stories that get NASA plastered to them, it’s got a lot of people rather riled up and for a lot of different reasons. Read on and I’m sure you’ll see why.

This is a fantastic story, I’ve never seen so many mistakes made by so many people in so many different ways, it’s quite a feat of engineering really. Also it does go to show that some people really do never learn. The roots of this story lie all the way back in 1997 when NASA scientists reported finding bacterial fossils in a meteorite from Mars.

This astonishing and revolutionary finding was reported by Richard B. Hoover who works at NASA’s Marshall Space Flight Centre. This was discounted shortly afterwards when it became apparent that the structures observed were probably contaminants from the time the sample spent on Earth before being studied. Now some people would learn from such a colossal mistake that was a huge embarrassment for NASA and Hoover personally.

This bacterium from Earth looks strangely like some observed in these meteorites (source)

Hoover, however, is made of stronger stuff. After his error in 1997 I’d like to say that he improved his working scheme, ensuring all samples were properly sterilised and cross checked before announcing proof of alien life to the public. But he didn’t. He returned in 2007, although with less impact (mainly due to lack of a successful publication), to say that he really had found life, this time in a totally different type of meteorite. Thankfully this time he attracted less attention.

Now, to the delight of many, Richard B. Hoover has returned to the public stage, thanks in no small part to the lovely people at FOX news, with another attempt. He’s still looking at the same rocks from 2007 but this time he REALLY thinks he’s got it.

Sunday, 27 February 2011

SOS: Save our Science - Drink Hearty Lads (and Ladies)

ResearchBlogging.orgHi Everyone. Hope there's still people out there reading this. Would be great to hear from you. Sorry things have been a bit slow, there's a lot going on this term, which I hope to write about (in part) soon. This new rotation is really fun, although quite long hours, and I've got loads of other projects going on relating to Science Communication, as many of you may already be aware. It means I'm not getting much time to sit and write articles on here though. I will be working hard to try and get back to ClearSci as much as possible, so hopefully more will be going on around here.

Anyway, so here's a fun story that is an issue I've been looking forward to having a go at. Everyone always has some new story about how alcohol is good for you or bad for you, and usually it depends on what you measure and whether it's the alcohol itself or something else (e.g. tannins in red wine) which is helping you out. This latest is cool because it pulls together a lot of research from the last 30 years, and actually finds some benefits, in certain instances, but also points out the importance of moderation. Enjoy. :)

This is a debate that I find quite interesting, especially since everyone seems to be more than a little biased in their desired outcome. It is the endless search for positive effects of drinking alcohol. A new meta-analysis (re-examination of lots of old data from different studies) of alcohol research may finally be able to put part of this issue to rest.

Tuesday, 1 February 2011

SOS: Save our Science - Bug Battle

ResearchBlogging.orgThis post was a request from a reader (Yay!). I've got a lot of different projects going on at the moment so have been a bit slow with the posting. Hopefully I'll be posting about my latest lab soon. There's still a lot to write when I get the time. We had a lot of fun last week meeting the students interviewing to join my course next year and the lab work is going well. There is a much more theoretical element to it, which I've been enjoying. Anyway, so this is a bit of a proto-story really. A possible explanation for the disappearance of bees worldwide; though the real science is still under wraps.
A honeybee (Apis mellifera) (source)

Pollinating insects, like bees, are disappearing across the world. The phenomenon is known as colony collapse disorder (CCD). If CCD continues as it is the world stands to lose most, if not all, pollinating species, which stands to rapidly wipe out all flowering plant species and would severely alter every land based ecosystem. A key element in understanding CCD was uncovered over two years ago, but is only just emerging as published work.

CCD is being studied by a dedicated group of researchers in the US Department of Agriculture’s Bee Research Lab. The rapid decline in colonies of pollinating insects due to CCD was originally observed in the US but has since been identified around the globe, though it has yet to arrive in some countries, including the UK.

Friday, 21 January 2011

SOS: Save our Science - Seeing Sharks!!
This is the end of my first week in the second lab, it's pretty fun so far, quite enjoying the variety of things I've become involved in and will hopefully get some very exciting data. It's going to be a busy term though. Anyway, more on that later. Here's some fishy news from Australia!

It is a commonly quoted fact that sharks can smell a single drop of blood in over 100 litres of water. As a top predator a shark needs highly developed senses to hunt, so it is surprising that many species are probably completely colour blind! Sharks still have excellent vision, but it is monochromatic i.e. Black and white.

The blacktip reef shark (Carcharhinus melanopterus), one of the species in the study, which lacks cone cells (source)

Sunday, 16 January 2011

SOS: Save our Science - Preventing Pandemic

Hey! I've been busy finishing my first project and after some last minute panicking it's all over and I'm moving on from chickens to yeast, but before I do I wanted to share this new story. A breakthrough in preventing the spread of Bird Flu, that has applications in protecting against a wide range of other viruses. This is the sort of story I've been looking forward to writing for a while, I hope you'll see why.

A group of researchers may have found a way to prevent the spread of bird flu through domestic populations, a revolution which could significantly reduce the risk of humans becoming infected. Not only that, but this technique could be easily used to protect against any viral infection in almost any species. It could even eventually be used to protect ourselves. This method requires no vaccinations and provides life-long protection from a broad range of different avian flu strains.

Tuesday, 4 January 2011

SOS: Save our Science - Cryptochrome, lord of time.

 I knew it'd happen sooner or later, I've started falling behind on postings. I'd hoped to put this up on New Year, but that didn't happen. Anyway, Happy New Year to all, hope you all enjoyed yourselves. I've been writing the report on my first project. The first draft is now done. Still a lot to do, and only 1.5 weeks until it's back to work. The next project is all about cytoskeleton and growth in yeast, so a bit different, I'll tell you more once I actually know anything...

So this is a relatively new paper I found, investigating how flies, and possible humans keep track of the time of day and how this is affected by our environment i.e. the sun. It seemed appropriate to do a time piece to see in the new year. Also I'm really excited as this will be my first official Research Blogging post!!

How do you know if it’s day or night? Simple, right? You look at your watch or you look outside. The differences are pretty obvious. But your body actually keeps track of these things itself. Certain proteins in your body keep track of the time of day. This system has been around for billions of years, and is shared between plants and animals.

The subconscious ability to tell night and day depends on circadian rhythms; regular changes in the presence and activity of timekeeper proteins within a part of your brain called the pineal gland (so named because it looks like a pine cone). Experiments have shown that in a room with no clocks and no changes in light levels a human will fall into a roughly 24 hour cycle of sleeping and waking (average 24 hours 11 mins). The average cycle differs between species and in some arctic species appears to be intermittent. Although the cycle is entirely self-sustaining it is trained and altered by light input, modifying it to be more exactly 24 hours long. This involves light sensitive proteins in your eye which signal to the pineal gland.