It’s Alive!

Apparently the US presidential candidates have better and more important things to discuss then the future of Science in the US. (HT to Kiwiblog for the vid)

*disillusioned sigh*

Hadn’t seen this for ages and ages, hat tip to Chocolate Bobka for the trip down memory lane…

This is effective teaching at its best. Complete with the catchy tunes, bright colours, and general epilepsy-inducing flashiness that only someone on a lot of drugs could come up with. Sigh, those were the days.

Some poor kid back in NZ became the latest victim of video game imitation violence as some joker, possibly trying to recreate the popular Sega game Sonic The Hedgehog, hurled a live hedgehog at him. This from the BBC:

“It hit the victim in the leg, causing a large, red welt and several puncture marks,” said Senior Sgt Bruce Jenkins, in the North Island town of Whakatane.

And you gotta love this quote from the same copper:

The police spokesman said the suspect was arrested “for assault with a weapon, namely the hedgehog.”

Tragically the poor, defenceless (well…) hedgehog did not survive the ordeal. God speed little guy.

Like most sciency types I know, I love talking about my research. The slightest provocation can launch me into a coma inducing rant about the minutia of my field (which has successfully terminated my chances of picking up non-sciency girls on a number of occasions). The normal responses to this rant (when the listener is still conscious) can be grouped into two categories.

The first response is the good one. It’s the one where my head grows to about 10 times its size as the listener goes on to commend the noble nature of my research and how the world needs more people like me interested in making a difference and not caring about money (one of which is true, one of which is not. I’ll leave you to decide). This comment is especially good to receive in front of any girls I may be trying to impress because then I can start acting all modest, yet still maintaining an air of selflessness about what I do. Chicks love that stuff.

Unfortunately, this response is usually followed by a second. The “I feel your work is important because my mum/dad/brother/sister/best-friend-forever died of cancer recently” response. I’ve had this said to me a number of times and never know how to reply, so an excruciatingly awkward moment of silence always ensues. This one is particularly bad to receive in front of any girls I may be trying to impress because it shows how I am both insensitive and slightly awkward.

I’m one of the fortunate few who hasn’t had cancer affect anybody I’m particularly close with (knock on wood) and thus haven’t had to deal with the raft of emotions that people go through when the disease makes an appearance in their or their loved one’s lives. Aside from my general awkwardness, I think the fact that I haven’t had intimate dealings with cancer is partly responsible for my inability to talk about it at a personal or caring-and-sharing level. But it’s not the only reason.

This is exemplified by something that happened to me yesterday. A colleague from uni back in NZ was recently diagnosed with cancer, so myself and another expat living here in the UK decided to send her a card, and this is where I hit a brick wall. What do you actually say to someone who has cancer?

Sorry you’re dying? Get well soon? Hope you like wearing hats?

Turns out I’m not alone here. Talking about cancer, even for doctors who have been doing it for longer than they care to remember, is not easy. At the end of the day, I think this really comes down to confidence and sensitivity. Talking about death is something people usually tip-toe around, and is definitely the sort of thing I try to avoid, but in order to get at the crux of why I research what I research I think I need to pluck up the courage to change this. While the charities that fund cancer research publicise the importance of this research at length, I think it is much more important for the people like me who actually do the research are able to discuss its practical and individual relevance.

Free wireless rocks. Am sitting here on the train typing away as the dull and dreary british countryside speeds past. Have just spent the last 4 nights down in London visiting friends, catching some live music, being a touristy geek, and generally taking a break from working for a few days.

Arrived on Saturday evening to attend a kiwi mate’s going away party which ended with me getting lost at around 5am after a warehouse party somewhere in Hackney Wick. If you’re from London then you’ll know that Hackney is not the sort of area you want to be wandering around lost in. Especially at the end of a very big night out. Although it only took an outrageously expensive taxi ride to get me back to the safety of my mate’s comfy sofa.

After spending most of sunday recovering, the next few days were a whirlwind of museums, galleries, flat whites, catching up on the old days, and sleeping on a very flat inflatable mattress. A particular highlight was the Imperial War Museum. It’s an exceptionally well laid out and informative series of exhibits that cover a number of international conflicts (although mostly dedicated to WWI and II) in objective detail. Plus there are a bunch of big tanks and guns and planes in the main entrance.

I Ended my stay by catching one of my favourite New Zealand bands, The Brunettes (who I have mentioned previously), play a Not In Kansas Anymore night. The gig was at Under The West Way, which is definitely an interesting place. It’s a tres trendy music and design studio building with a cosy bar on the ground floor that has a very homely atmosphere reminiscent of certain bars I frequented back in Dunedin.

The gig, as with every Brunettes gig I’ve been to, was quite simply brilliant. While playing to a british audience is an endless battle for home-famous kiwi artists touring over this side of the world, it’s clear the delightful mix of angst, pop, and candyfloss that The Brunettes are renowned for had won the small crowd over from the second song. Despite having just come off an exhausting tour of the US, they managed to play an exceptionally tight set bursting with energy and enthusiasm. And I swayed along with the rest of the crowd in a constant state of awe at the unfaltering beauty of Heather, the lead singer. They head off now for a lengthy European tour finishing back up in London in a months time.

Over an end of semester dinner with classmates last night I encountered what I had always thought impossible: a frank and honest discussion about religion that didn’t end in me wanting to slap someone in frustration. In fact, I would go so far as to say that I found it profoundly insightful.

I’m an avid Pharyngula reader and a big Dawkins fan, but usually steer clear of the Science vs Religion debates that are awash throughout the blogosphere. Not because I don’t have an opinion, but because it’s a huge topic area and for the most part I just can’t be bothered. Also, it always seems to be the same stuff going around and around ad nauseum.

And it’s for these same reasons that religion doesn’t usually form part of my dinner time conversation repertoire. It’s more the domain of drunken ranting, particularly with one of said classmates who I have enjoyed numerous alcohol induced religious arguments with.

My classmates are all very smart, knowledgeable and critical young scientists, but I did not really understand how this could be reconciled with their religious beliefs (they’re all Catholic) until our conversation last night. It turns out that their beliefs are much more rational than I had preconceived.

At the root of it, their concept of God is pretty much the same as my concept of the scientifically unknown. They believe in evolution, the big bang, and explaining natural phenomena through science. They do not believe God dictates their actions or controls their destinies, and they do not pray for divine intervention in the minutia of their daily lives.

The only real difference between myself and them is that I don’t mind the idea that the universe is the be all and end all (in fact, I live in a constant state of awe at this concept), while they find a wee bit of comfort in thinking that beyond all this there is some divine force that they just so happen to call God.

I can sympathise with this concept of religion, and don’t find it that irrational. I don’t really see a huge disparity between believing that beyond the ends of the universe there exists either nothing or some omnipotent force. The concept of god does not explain the universe, it just exists as a sort of mental safety net for when we get beyond the bounds of our imagination. I don’t believe it, but I can understand why so many people do.

Importantly, this discussion also helped me to realise that it’s probably not the best idea to lay my preconceptions about religion on anybody who calls themselves a christian. While I do have a fairly sound understanding of christianity (I went to a Catholic school AND i’ve read The Da Vinci Code) I have been reading Dawkins and PZ Myers for way too long without stopping to think that not all religious types are irrational and close minded.

That said, the rational academic christian is definitely in a different league to the crazed religious zealots that mascarade their doctrines as pseudo scientific theory.

(new edit: A similar conclusion is drawn after a hefty yet eloquent discussion on the philosophy of science by Dr Freeride)

My MSc thesis is now on the shelf in the University of Otago medical library, almost six months after I first submitted it for examining. Unfortunately, receiving it back from the examiners last year coincided with my shift over to Edinburgh, so making the suggested corrections and formally submitting it took a bit of a back seat to drinking, making new friends, and starting a PhD.

But now it is sitting in the dark, musty, windowless thesis room deep in the bowels of the library, just waiting to impart its awesome glory on whoever stumbles accross it.

Continuing my new trend of spending waay too much time trying to finish my lab work for the semester instead of being permanently connected to my laptop, I only have time today for a brief video post on the theme of science and dancing.

As anybody reading this will likely know, the Youtube video Evolution Of Dance is oft quoted as the most popular YouTube video of all time, with over 78 million page views.

But now, I think we may have a new contender.This video takes everything good about the aforementioned video, and makes it better. How does it do this? Simply by replacing the guy with arguably the best robot ever: Optimus Prime.

Why this has only received a meagre 200,000 views to date is quite beyond me.

Although fortunately a friend from back home sent me the latest album from one of my favourite NZ bands, the Phoenix Foundation, entitled Happy Ending, which has helped keep me from jumping out the lab window.

I’m drawing to the close of my research project for the semester so am obviously spending this week doing all the experiments I should have been doing for the past two months in a mad attempt to get enough data to write a coherent report about. Have spent 12 hours or so every day this week doing nothing but HPLC to measure the effects of up or down regulation of a particular serotonin receptor (5HT2CR…if you’re asking) in a couple of lines of transgenic mice we have in the lab. While interesting in theory, the actual lab work involved in preparing and running each sample is very mundane, thus this album was a welcome addition to the lab-work playlist on my iPod.

And since these experiments have cut the umbilical cord I share with my laptop on most days, this post is all I have had time to come up with all week (which is a token effort, at best). Anyways, here’s the retro-tastic beast of a video clip for the first single off said album, Bright Grey.

If baldness is really a genetic trait, then I am well and truly screwed. I come from a long line of cue balls; every male in my family over the age of 30 is bald or balding. Especially worrying is the fact that both my Dad and my maternal Grandfather started thinning in their mid twenties, a fact my Dad takes particular glee in pointing out to me at every available opportunity.

Thus, I greeted a couple of recent articles in Nature Genetics with an air of optimistic hope. Of particular interest to me is the paper by Pasternack et al (citation below), which details a complete a start-to-finish study on the genetics of a rare hair loss disorder, beginning with a genome wide linkage analysis and ending in functional characterisation of the candidate gene: P2Y5. A simultaneous article in the same journal also looked at the involvement of this gene in hair growth, but from a different functional perspective, as covered over at Gene Expression.

Due to the commonality of baldness and the complex pathophysiology of hair growth disorders, finding a genetic cause with therapeutic potential is extremely difficult. This is why studying rare heritable hair loss disorders, such as the specific alopecia condition analysed in this study, offers a unique opportunity to pinpoint some of the key components involved in maintaining normal hair growth.

A powerful approach to advance our understanding of the pathophysiology of human hair loss is to identify genes underlying mendelian isolated alopecias. Investigation of this type of hair loss offers the unique opportunity to identify factors that are not only necessary for, but also specific to, hair growth.

Using an affected Saudi Arabian family, the group mapped the disease locus to a 28Mb region on chromosome 13. Candidate gene sequencing revealed a truncating mutation in the sequence for P2Y5: a gene that codes for a G protein-coupled transmembrane receptor. Normally located on the cell membrane, the group showed accumulation of the truncated protein in the endoplasmic reticulum, suggesting loss of function.

Aside from the solid genetic analysis carried out, the real strength of this paper lies in the further functional analysis of the protein, which did not have a clearly understood function. Through a reporter gene assay and A radiolabelled binding experiment, the group identified lysophosphatidic acid (LPA) as the ligand for the receptor. In addition, they demonstrated in vitro that the truncated version of this protein is unable to elicit the cellular response normally observed after binding of LPA to P2Y5, likely due to the loss of a number of intra-cellular loops that are known to be involved in G protein activation.

LPA is known to bind a number of receptors alongside P2Y5, with a downsteam effect of enhanced cell proliferation and migration. Broadly, these receptors can be classified into two subgroups: LPA1, LPA2 and LPA3 in one group, and LPA4 and LPA5 in the second group. The authors propose the placement of P2Y5 in with this latter subgroup due to its amino acid sequence homology and the similar downstream signalling pathways.

Interestingly, of the latter group of receptors, LPA4 and LPA5 are not expressed in the hair follicle. Thus, a loss of the one member of the group that is, P2Y5, leads to a complete loss of LPA signal transduction through the specific pathway mediated by the group. Further characterisation of this pathway is now required in order to understand how its impairment results in the alopecia phenotype observed in affected individuals however.

Ultimately, the most important question to arise from this study to me is: could it eventually culminate in an effective treatment (or even a cure!) for baldness? While it is conceivable that this paper offers the possibility of identifying potential inducers of the LPA-P2Y5 mediated pathway in a hope of enhancing hair growth in balding individuals, more realistically it offers potential for further elucidation of the complex pathways involved in hair follicle development and function.

Thus, I don’t think I’ll be seeing any wonder-drugs in the crucial next few good-hair years I have left in me that will cease the inevitable chrome-domia before it advances into chronic cue ball-ness.

Pasternack, S.M., von Kugelgen, I., Aboud, K.A., Lee, Y., Ruschendorf, F., Voss, K., Hillmer, A.M., Molderings, G.J., Franz, T., Ramirez, A., Nurnberg, P., Nothen, M.M., Betz, R.C. (2008). G protein-coupled receptor P2Y5 and its ligand LPA are involved in maintenance of human hair growth. Nature Genetics, 40(3), 329-334. DOI: 10.1038/ng.84