6 word autobiography meme

Another day, another meme! This one is from ScienceGirl, and here are the instructions:

1. Write your own six word memoir

2. Post it on your blog and include a visual illustration if you’d like

3. Link to the person that tagged you in your post and to this original post if possible so we can track it as it travels across the blogosphere

4. Tag five more blogs with links

5. And don’t forget to leave a comment on the tagged blogs with an invitation to play

The first one that comes to mind is:

Love blogging but suck at memes

Seriously though, this is tough. If I’d been asked for one sentence it would have been easy:

“It’s better to regret doing something, than to regret not doing it”.

I can’t seem to distill that though.

Maybe it’ll be easier if I break this down into separate areas of my life.

My career:

Left academia, missed it, came back
My decision to apply to stay in Canada after my initial 2 year work visa expired:

Came for job, stayed for men

(well, one man in particular, but men is funnier. Yes, that’s me in the photo, taken in 2002 before I met Mr E Man!)

Talking of which, Mr E Man inadvertently came up with his own 6 word biography of me on Sunday. I was trying to talk to him about a certain excellent football result while he was watching The Godfather, which wasn’t going down too well.

He said something like, “this is a very complex plot and I need to make sure I don’t miss anything important”.

I replied, “well, I’m very complex too, maybe you should make sure you don’t miss anything important that I say”.

He replied, “you’re not complex and I won’t miss anything important. It’ll just be Newcastle blah blah science blah blah“.

To sum up:

You’re funny; divorce lawyer on standby.

Erm, tags… if you’d like to join in, please consider yourself tagged! Is that OK?

Posted in career, meme, personal, photos, silliness, sport | 11 Comments

Foolish dreams

So I had this crazy hilarious dream last week, but decided to keep it for April Fool’s day.

In my dream, I was round at my friends’ house when an alien spaceship crash-landed in their garden. We called it in to the police, but they wouldn’t believe us because it was April Fool’s day and the local news team were running a similar story as a prank. We turned on the news, and they were indeed all dressed as Imperial Stormtroopers and running around pretending to panic.

So we had to deal with the crashed spaceship all on our own. I woke up laughing before the aliens came out though.

Dreams absolutely fascinate me. I’ve never read a convincing explanation of what they’re for, but even if they turn out to be completely useless I wouldn’t give them up for anything. My favourites are the ones where I suddenly realise that I’m dreaming, but don’t wake up, so I get to direct what happens. I usually end up flying in those dreams.

Has anyone spotted any good April Fool’s stories today? I’ve seen a couple, but they’re really obvious. The comments thread on my post about lab-based practical jokes contains some excellent suggestions if you’re heading into work with mischief on your mind.
__________

Update: I just spotted Nature’s contribution to the festivities. And how could I have forgotten to check what Google are up to today? Apparently, “Well, you’re distressingly normal and could conceivably adjust to life as a deep space pioneer, though we recommend instead that you leave the Mars missions to the serious whack jobs who scored over 130 and instead finish year 3 of law school, tuck your toddler into bed, design Web 2.0 applications, run for Congress or do whatever other normal, healthy, middle-of-the-road thing you’re currently doing with your normal, healthy, middle-of-the-road life. If you’re determined to give Virgle a try, though, you can submit your video here.”

Posted in personal, silliness | 9 Comments

Ashtrays and Atheists

The province of British Columbia introduced some new anti-smoking laws today. The city of Vancouver is taking things to an extreme – cue reporters on the morning news measuring exactly how far you have to be from a doorway before you can light up. The answer seems to be “in the road”.
I’m a life-long non-smoker who has already benefited greatly from BC’s previous laws, which prohibited smoking inside bars and restaurants. Moving here from Glasgow in 2002 brought instant relief from having to wash my hair as soon as I got home from a night out, and my clothes after every use. Now that the UK has its own smoking ban in place, going home is much more pleasant than it used to be and I am no longer addicted to second hand smoke. (I swear when I first moved here I used to inhale deeply every time I passed a smoker).
So I should be delighted with the new laws, right?
Wrong.

Continue reading

Posted in Uncategorized | 34 Comments

Archive meme

Oh dear, I’ve fallen a long way behind on my memes. Apologies to people who’ve tagged me, I haven’t forgotten!

The Archive meme came from Mad Hatter and ScienceGirl. Here are the instructions:

Go back through your archives and post the links to your five favorite blog posts that you’ve written. … but there is a catch:

Link 1 must be about family.
Link 2 must be about friends.
Link 3 must be about yourself, who you are… what you’re all about.
Link 4 must be about something you love.
Link 5 can be anything you choose.

I think this is a great way to circulate some of the great older posts everyone had written, return to a few great places in our memories and also learn a little something about ourselves and each other that we may not know.

Post your five links and then tag five other people. At least TWO of the people you tag must be newer acquaintances so that you get to know each other better….and don’t forget to read the archive posts and leave comments!

This has been a really tough one for me. I don’t really tend to blog about my friends and family, although there have been a couple of recent exceptions. But surely the point isn’t to link to recent posts…

Hmm, to solve this dilemma I think I’m going to have to cheat a bit!

1: Family
Here come the cheating! Our biological family is Hominidae, which includes humans, chimpanzees, bonobos, gorillas, and orangutans. So here’s a Primate Party post about bonobos, which are awesome. Check out the blog the post links to – Vanessa’s gone quiet now, but it’s definitely worth reading her archives.

2: Friends
More cheating! Here’s a post on my Nature Network blog about the friendships I’ve made during my career, and what happened to them when people moved on to new cities and countries.

3: Myself, who I am… what I’m all about
This one’s a little easier! Here’s one of my first posts, describing why I got into science. I think it says a lot about who I am!

4: Something I love
I love men in kilts, but you already knew that. I also love clever wordplay and geeky science humour. Here’s an example; I just wish I could take credit for it.

5: Anything…
Hmm, I really should have saved the rehash of the ERV triumph for this meme. I may as well complete the theme that I started with #3, so here’s the post that originally followed it. The subject is “Why I got out of research”.

Phew, that was tough! This post took me ages! Hopefully the next one will be easier. Sum up your life story in 6 words, yeah, piece of cake!

I won’t tag anyone because this is such an old meme and I think I’ve read it just about everywhere already. I am not exactly an early adopter!

Posted in meme, personal | 1 Comment

Guest post (not for the squeamish)

My friend Kyrsten has supplied me with a couple of interesting blog post subjects in the past, and I’m going to let her tell this current story in her own words. (What this essentially means is that I’m going to copy and paste (with permission) from the emails she sent me this week). Hopefully this will be her only personal contribution to my “medicine” and “freakishness” tag counts.

When I say “not for the squeamish”, I do mean it. My initial response was (and I quote): “fucking hell Kyrsten, that’s disgusting”. It took me several hours to get to “it is kinda cool though”. Of course, by the next day I was asking if I could put it on my blog! Anyway, the photos are down at the bottom so you don’t have to look if you don’t want to.

Take it away, KJ:
_______________

“Hi guys,

Caution, if you aren’t a medical doctor (some of you are) and thus get squeamish easily, don’t read on. But you are all scientists for the most part and should find this cool like I did (now that Bob is gone!)

As some of you may know, I recently went to Belize for a week with three of my friends, and we stayed in the jungle for 3 nights and on the beach for 4 nights. In the jungle (which was amazing), we went on a small day hike. Being mostly prudent, I made sure to cover my body in DEET and wore a long sleeve shirt and pants. The only area i didn’t cover was my rear and near the bikini line, because those would have to be some crazy mosquitos! WELL. The jungle sure is full of bugs, as the ones of you that travel tropically well know. I come back with a few mosquito bits – in the area I didn’t cover with DEET (and quite a few in the area i did cover) but don’t think much about it.

I get back and everything is peachy – no one has dengue, none of us are sick, and it was a great vacation. Except I have what I pass off as an ingrown hair near my bikini line. It gets larger, and it’s not healing properly. I get these weird, periodic stabbing pains that I think is a staph abscess getting worse. They are rare, but when they do happen, they make me double over in pain. They kinda freak me out after three bouts of pain, a days apart each, so I slather it in polysporin, bandage it, and go to my GP. He takes a look and proclaims it as an ingrown hair that is infected, and injects the area with lidocaine and cuts it to drain it. In an abscess, you would expect to see a pocket of pus (white blood cells that have gone to fight the infection and died), but there was no pus – which he finds odd. He gives me a prescription for cloxacillin and says to keep an eye on it and see him in a week.

I take the antibiotics as prescribed, and there isn’t any more change except it’s not healing. On Friday after working an 11 hr day, I sit down, and notice that there is something sticking out of the hole – looks flesh coloured like a piece of skin. I touch it when the tip of my nail and IT RETRACTS into a 1-2 mm hole in the middle of the inflamed area. Immediately I start screaming, and D takes one look at my white face and wants to know if I’d like to go to Emerg (no clinic open at 8 pm on Good Friday). I see the R1, and he asks me some questions, and then takes the doctor in. At this point, i have no idea whether it’s still bacterial or not – but I was pretty convinced it was parasitic – S. aureus doesn’t ‘wave’ at you and retract into a HOLE! I was also so exhausted from being up since 5 am that morning that I wasn’t sure if I hallucinated. The doctor is hesitant about doing anything to it, and says to stay on antibiotics and come back if it gets worse. I can’t sleep at all because I have thoughts of chopping off my leg, and decide to google search parasites that might cause periodic pain, be from Belize, and cause a hole in the skin – and come up with Botfly! I find 100s of stories of people who go to Belize, Panama, Costa Rica, Brazil and come back with Botflies – most of them from Belize though. The symptoms are all eerily similar.

After sleeping a grand total of 2 hrs, I get up and take a look. Again, there is this 1 mm diameter fleshy looking thing on the top of the wound! again, it retracts into the hole. D says he can’t take 4 more days of me panicking and that it’s time to go back to Emerg. I decide that it’s coming out THAT DAY. I go to emerg, they admit me, and I start talking with the head nurse – she thought the previous night that I was misdiagnosed and that it was botfly, from what she’s read. The doctor on hand is Dr. G and as soon as he hears ‘parasite’ he gets all excited – he used to do some tropical medicine (treated dengue in his early years). I had printed off info from what i found on the web, and he determines that most people do is suffocate the botfly as it needs to breathe to complete it’s life cycle. So we slather on a petroleum product, cover with an airproof and waterproof bandage, and they send me home. I’m told to come back when the botfly stops moving. After about 1/2 hr, i can see the botfly’s breathing tube moving around in the petroleum. Interestingly, it’s also throwing other stuff out of the hole so the petroleum looks weird and clumpy. I decide that there is no way I’m letting the Botfly this one so I decide to wait as long as I can (I’ve named him Bob the Botfly at this point, a friend said his middle name should be Ro so he could be Bob Ro Botfly but that’s just weird). I hang out, and decide to relax and try to breathe – not easy when you are pretty certain that there’s something growing inside you.

This morning, I get up and we go to Emerg. Dr. G is there from yesterday, and this time he’s got Z the R4 who’s never heard of botfly. During my relaxation time yesterday I googled as much clinical info as I could find, and found a great paper from Kevin Kain who runs the Tropical Infectious program at U of Toronto. Print it out and brought it in with me, highlighted the info they needed. Z took a look at it, summarized it for Dr. G – they pull off the bandage, and immediately Dr. G sees the parasite – he grabs it with the forceps and pulls it out (hurt a little because the hole was only about 2 mm, whereas the parasite at its biggest was about 4 mm in diameter. Cleans me up, puts a little bandage on and I’ll continue the antibiotics I’m already on to stop any infection, but things should be fine.

I’ve attached a few photos of the bugger. We have an old antique microscope at home, so D and I have been taking a look at it under the microscope. pretty cool! Some of the black spines have my skin cells on them 🙂

I’m kinda proud of my Bob the Bot Fly. I don’t have any formaldehyde here so can’t preserve him, but I think the pictures are more than enough.

Will this stop me from going to Belize again? hell no! The place was amazing and I know what to look for now :)”
_______________
A subsequent email reads:

“I am still alternating between “OMIGOD THAT WAS IN ME!” and “WOW! CHECK OUT THOSE SPINES! What evolutionary path led to THAT?!?””

Later:

About the blog, you can definitely talk about me on it – i’m ok. But you have to promise to put up the story of how I found the article myself and diagnosed myself :)”

I love geeks.

Anyway, here are a couple of photos of Bob. The coin is a Canadian dime, about the same size as the US equivalent or a British 5 p coin. Judging by the series of photos on this blog post, Kyrsten was very lucky to have noticed him so early in his life cycle!



OK, I’m done grossing you out now. If you’d like to leave a comment or question for Kyrsten, I’ll let her know and I’m sure she’d be happy to answer. The next post will be less disgusting, I promise!

Posted in freakishness, medicine, nature, photos | 11 Comments

Not hardly that one, Volkswagen XY NOT

Here is a serial translation of my "About Me" text, brought to you by Lost in Translation via Brian Clegg at Popsci on the Nature Network. This version dragged the text on a tour of Europe, translating it into French, German, Italian, Portuguese and Spanish, with a translation back into English in between each foreign language version:

"A degree in genetics executed the PhD in the molecular Biology of the batteries. PhD executed to postdoc in being human of history WITH of gene and to the papers of the operation of the Canadian. Postdoc executed to a work of the industry and the way-resident-permanent one. The work of the industry executed for disattenzione of my brain of science. With blog that begins my brain of science must protect and helped the new work that the returns for him are of the concession of the academic writing are executed. With blog that it continues it executed to me invites that blog still begins in the network of the nature. Who knows, this what arrests the future? Continuous with the Blogging and me it discovers. How Douglas wrote to Adam in the later one, Volkswagen XY NO?"

Here's what happened when I checked the "Include Chinese, Japanese and Korean" button:

"The member of the genetics has lead that cytobiology the PhD. PhD has obtained to postdoc, works allowed with development of Canada of the chromosomes of the person through. Postdoc has obtained the jobs of the company and the condition of the personal of the definitive room. The jobs of the obtained company have neglected my scientific brain. To the summer, than the worries that the beginning cronometra my brain of blog science they have been insured persons, found is tying and he, the job in order to take itself, that it has been produced recently from the writing of the subsidy of science the situation for support. To blog in order obtaining the continuation, it has begun I recently invite it manufactured of the network of the character of blog. A sure person knows that this conservation sends? Continuous to observe the Blogging in on. Not hardly that one, Volkswagen XY NOT 6a to you ' 6a in the writing. 6a. 6a '. Return of the Douglas?"

Return of the Douglas would be fantastic. Maybe in some other universe.

I have no idea what's up with the font by the way. I'm hoping that if I ignore it, it'll go away.

Posted in English language, meta, silliness | 10 Comments

Endogenous retroviruses and evolution: redux

While chatting with Propter Doc last week, I realised that most of my current readers weren’t around to witness this blog’s finest hour. Way back in June 2007, I posted an explanation of why a paper of mine that had appeared on a creationist website actually provided evidence in support of evolution. The post earned me many links, including one from PZ Myers at Pharyngula* (as Propter said, it’s like getting a link from God! I got an email too!). It also made the front page of Reddit; these two internet forces combined to bring in over 3,000 unique visitors in one day. The post also spawned a crazy comments thread, featuring some nice juicy arguments with creationists (you can see it here at the original post), and is the most frequently Googled post on the entire blog. As my sidebar poll comes to a close, more than 50% of all respondents have indicated that they planned to use the material in the post in their own arguments with creationists. In fact I’ve already seen the link appear in several internet discussion forums.

Oh, and they eventually took my paper off the website: details here. Score!

The text of the original post is below if you’re interested…

*Another conversation with Propter: is it Pha-RING-you-lah (my interpretation) or Pha-rin-GOOL-ah (hers?)
____________________________________________

Here is my description of the part of my research that has been misrepresented by the Reasons to Believe website. See this post for an explanation.

My paper concerns the regulation of a human gene by DNA derived from an endogenous retrovirus (ERV). An ERV is a viral sequence that has become part of the infected animal’s genome. Upon entering a cell, a retrovirus copies its RNA genome into DNA, and inserts the DNA copy into one of the host cell’s chromosomes. Different retroviruses target different species and types of host cells; the retrovirus only becomes endogenous if it inserts into a cell whose chromosomes will be inherited by the next generation, i.e. an ovum or sperm cell. The offspring of the infected individual will have a copy of the ERV in the same place in the same chromosome in every single one of their cells.

This happens more often than you might think; 8% of the modern human genome is derived from ERVs. Repeated sequences of this kind were formerly considered to be non-functional, or “junk” DNA. However, we’re gradually finding more and more examples of viral sequences that appear to have some kind of function in human cells. For example, many ERV sequences play a role in human gene regulation. ERVs contain viral genes, and also sequences – known as promoters – that dictate when those genes should be switched on. When an ERV inserts into the host’s chromosome, its promoter can start to interfere with the regulation of any nearby human genes. In the example that I researched, the ERV promoter has become responsible for most of the expression of a particular human gene in the large intestine.

Creationists and intelligent design advocates like to think that because some ERVs have useful functions in the human genome, they must have been deliberately put there by a creator / designer with that particular purpose in mind. Of course, no-one can explicitly prove that that is incorrect – it’s not a falsifiable hypothesis, and therefore it’s not science. What we can show is that ERVs provide evidence in support of the theory of evolution.

Let’s imagine how ERVs would behave within a model of evolution by common descent. An ancient creature, let’s call it the common ancestor of all modern mammals, is infected by a retrovirus that becomes endogenous. All of the animal’s descendants (i.e. all mammals) would be expected to carry the same ERV insertion (ERV1) in the same chromosomal location.

Fast forward in evolutionary time. Different lineages have evolved and diverged from the original common ancestor and there are now many different types of mammal in existence, all carrying ERV1. A small rodent, let’s call it the common ancestor of mice and rats, is again infected by a species-specific retrovirus that becomes endogenous. This is ERV2. In a parallel event in a different lineage, the common ancestor of all great apes acquires a third insertion, ERV3.

Moving forward again, a fourth ERV appears in some of these new-fangled human thingies that are running around in Africa, but not in their hairier relatives who will eventually evolve into modern chimpanzees. The early humans spread out, and a fifth and (don’t worry) final ERV arises in a population that is isolated in a discrete geographical location. The infection does not spread to other human populations.

So what would we expect? Humans, chimps, mice and rats should all possess ERV1. The mouse and rat genomes will also contain ERV2, the virus that infected their common ancestor, but not the primate-specific ERV3, 4 or 5 insertions. All great apes will share an identical ERV3 insertion; all humans will also possess an ERV4 insertion that is not found in chimps or other apes. In addition, some, but not all, humans will carry an insertion of ERV5. The rodent-specific ERV2 insertion will not be found in any primate species.

Now that several genomes have been sequenced, we have begun to test these predictions. The patterns of ERV insertions observed in modern species exactly match the predictions made by the model described above. Some insertions are shared between humans and mice and represent truly ancient viral infections. Others are found only in primates, and not in other species, obviously derived from an infection of the ancestral primate species after its divergence from other lineages. More modern insertions are found only in humans, while the youngest ERVs of all are found in some humans, but not in all. We do not find any examples of ERV insertions shared by, say, humans and mice, but not by chimps. Insertions are always shared by all species, and only by those species, that have a common ancestor. ERV insertions therefore provide excellent support for the theory of evolution by common descent.

My particular favourite ERV is found in various primate species, and therefore must be at least 25 – 30 million years old. I compared the sequences and activities of the same ERV promoter in the human, chimp, gorilla, and baboon genomes. Despite some minor “single-letter” point mutations caused by DNA copying errors, the promoter had essentially the same function in all four species. I struggle to understand why any kind of designer would decide to use different codes to perform the same function in different species, but there it is. I hypothesised that the ERV was only allowed to persist (that is, its meddling in gene regulation didn’t kill the first organism in which it inserted, which was therefore able to pass the insertion on to its offspring) because the incoming ERV promoter behaved in a very similar way to the original host cell’s gene promoter. I wasn’t able to do the experiments I wanted in order to investigate this point, but another group subsequently did, and their findings supported my hypothesis. That’s what happens when you make and test falsifiable predictions.

I could go on and on about the role of ERVs in genome evolution, but this post is too long already. I would encourage anyone who’s interested to search for “endogenous retrovirus” AND evolution in the PubMed database of peer-reviewed research papers. You won’t find much in there about creationism or intelligent design.

Posted in creationism, evolution, meta, original research, science, virology | 11 Comments

The lament of the classical guitarist

Mr E Man and I visited his mother on BC’s Sunshine Coast at the weekend. As usual, the days were filled with good food, wine, reading, crosswords, Scrabble, and the occasional short hike (the weather was not living up to the promise of the region’s name).

It seems that we’re getting to know more and more people who live up there, including my brother-in-law’s hilarious new girlfriend (HNG) and her friend, who also used to work with Mr E Man and his father. (It’s that kind of place). On Saturday we were invited to their regular music night. We drove a short distance, clambered up a very dark and hilly driveway, and found ourselves in a semi-finished one room shack filled with a smoky blue haze and rockin’ blues music.

As I’ve mentioned before, my BIL is a roofer by day and a rock star by night. He’d brought his guitar and was giving it his all as usual*. There were 3 other guitars (no bass though, which was the only thing missing), a harmonica, the host at the drum kit, various others (including us – no passive spectators allowed!) on assorted percussion instruments, and BIL’s HNG on flute. The host’s wife, an award winning professional singer, was persuaded to belt out a few songs, with various other vocalists taking their turn. There was the occasional break for drinks, smokes, and a stumble in the dark to the scary steaming outhouse, but apart from that the music was continuous until we left at around midnight. It was just fantastic.

I was so jealous. I play the classical guitar, but unlike others (such as Wayfarer!) who start to play with the aim of being able to play around the campfire, I was taught very classically from an early age and while I can read music, I’ve never learned to improvise. I tried to jam with BIL once, with disastrous results – I don’t know the songs that people expect me to play, and I can’t just “transfer it to E minor, it’ll sound better”. I’ve got the wrong kind of brain or something, which is a shame because I just love playing music in a group.

I’ve spent a fair amount of time and energy recently trying to persuade some friends who play various instruments (flute / clarinet / trumpet, violin, and another classical guitar) to get together for a music-reading, classical version of the evening described above. I painted a picture of a small group of women who hadn’t played in a long time getting together once a month or so in a low stress, no guilt, wine infused setting to play music. I even offered to host, and Mr E Man had (not very reluctantly at all) agreed that he would go to the bar with his BFF on those nights. Naturally, everyone thought it was a great idea, but no-one actually wanted to do it just yet as they were “just so out of practice”. My assertion that we’re all in the same boat fell on deaf ears and I ended up telling people to practice for a month and I’d get back to them.

BIL’s HNG is really keen to join us, so I think it’s time to resurrect my idea. Maybe people will be more likely to come if I tell them that the two of us are doing it anyway, here’s the date and time, come if you want to.

Campfire optional.

*I’m proud to say that I beat him at Guitar Hero at Christmas!
____________________________________________

Appearing now at a Nature Network blog near you:
The effect of a peripatetic scientific lifestyle on friendships
April Fools pranks for your lab

Posted in music, personal | 14 Comments

Lab larks and April antics

In plenty of time for April Fools Day, may I present a thread on good practical jokes to play in labs?
.
Dry ice exploding out of snap-cap tubes is old hat. The snatching away of our secondary school chemistry teacher’s chalk with invisible cotton threads as she reached for it was fun, but generic and juvenile. I want to hear about the most creative and elaborate (OK, and safe) tricks you’ve ever seen played in a lab environment.

Continue reading

Posted in Uncategorized | 18 Comments

Leaving labs and losing labmates

I’ve been giving a lot of thought recently to the effects of a peripatetic scientific lifestyle on friendships. I spent my undergrad, postgrad and postdoctoral years in different countries, and in each place there was a constant reshuffling of my group of friends as some people moved on to new positions, and new recruits arrived to take their place. These days though I’m firmly settled in Vancouver, working in the same building in which I did my postdoctoral research. The company that employed me for the two years in between is about a three minute walk away. A new job no longer means a new location and a new group of friends.

Continue reading

Posted in Uncategorized | 4 Comments