I’m ready one hour early for the first day of my new job. I’ve got a new haircut, new shoes – I feel like a kid going back to school after the summer. All I’m missing is the new lunchbox with matching thermos.
It’s been a while since I was “the new girl”. Last time, I came home at the end of my first day and collapsed on the sofa, unable to answer the simplest question or form even short sentence fragments. It’s the one and only time my hubby has ever seen me lost for words.
Wish me luck!
Welcome to Mendel’s garden, and a fine day it is for some lovely genetics. And a game of football (you know, that game in which you move the ball with your foot, not that other no doubt worthy but definitely misnamed “throwball” game.) Hey, if philosophers can play, so can geneticists.
I’m here because I love genetics and football, but why have our other participants turned out? Matt Mealiffe MD is here because there’s nothing worth watching on TV. Live results of genetic tests for breast cancer susceptibility really are a new low in televised entertainment, and going outside to play is a much more sensible way to spend your time.
Wenchypoo is here for the health benefits of exercise. Knowing your family’s history of potentially genetic disease, and passing that information on to your kids, makes perfect sense in a world where health care is not universal. Good diet and lots of exercise are great ways to minimise the effects of any unhealthy genetic programming. If all else fails, we can always hope that the recent advances in biological data mining that David Hamilton has been telling us about will fulfill their promise of a better understanding of cancer and other diseases.
So that’s one vote for football-better-than-TV, and one vote for exercise. Does no-one else want to share? Fair enough. Eric Michael Johnson points out that a person’s involvement in processes such as voting may be genetically determined, so we shouldn’t blame ourselves too much. The motivation to participate in democratic processes may be a byproduct of our evolved ability to co-operate with others, so it will be interesting to see whether the people that spoke up just now will make better team players.
It’s getting cold out, so let’s get this game started! It’s Mendel’s garden, so we’ll let him kick off, even though I’m the only one who thought to bring a ball. (Luigi Guarino brought beer though. What a star! We’re all very appreciative that barley, like some other crop and livestock species, was domesticated multiple times by our ancestors.) The maverick monk gets us started, and he’s showing some nifty footwork for a religious man. Not quite the Hand of God, but some divine ball skills nonetheless. But the local favourite runs into a cloud of fruit flies and loses sight of the ball. He doesn’t look too happy, in fact he seems to be taking the non-Mendelian mode of Drosophila transposon inheritance a wee bit personally.
There’s always someone who brings a dog, and today it’s Archaeozoo. The dog takes the ball from the feet of the confused Mendel, and he’s off! Ha ha, how cute, very funny, give us the bloody ball back will you? But that there dog is descended from wolves who continued to interbreed with his ancestors for generations, and he’s got a bit of a wild streak. The game comes to a grinding halt, resuming only after two puncture wounds are bandaged up and the dog is safely tied to a tree.
Greg Laden cues up the ball for the restart and plays a nice ball into the box. He’s a very creative player, this one – or is he just reassembling existing moves into something that looks more creative than it is? Kind of like Craig Venter and artificial life? Hmmm. Let’s just admire Greg’s contribution to the beautiful game and leave the big questions to the philosophers on the next field over.
Eric picks up Greg’s pass and plays a nice little one-two with David. He turns on a dime in the box. He shoots, he scores! 1-0. What a great demonstration of teamwork and inter-primate co-operation. Our intrepid goalie, Grrl Scientist, protests that she was distracted by a gang of wasps who were showing their own kind of co-operation and scaring the bejeesus out of her and the rest of the defense. Wasps have evolved group maternal and reproductive behaviour, switching between the two as their gene expression patterns change, and now they’ve evolved the ability to disrupt major international sporting events. They’re worse than the bloody fruit flies. Maybe a garden is not the best place for this game.
The goal stands, regardless of insect interference, and the game resumes with a renewed passion as the other team tries to make amends. Dr Matt passes back to Grrl, who feeds the ball out to Luigi. Luigi nutmegs Mad Hatter – apparently defending against this feisty forward is almost as difficult as playing whac-a-mole with the constantly evolving polio virus – and threads the ball through to Wenchy, who’s in acres of space.
Sudip Ghosh makes an impressive sliding tackle that gets the ball but unfortunately knocks Wenchy over. It looks like he may have mistaken Wenchy for James Watson, but instead of getting a Nobel prize rescinded, all he achieves is a free kick for the opposing team. Wenchy takes a shot at goal, it looks good, oooohhhh! Jesus saves, but I score on the rebound. 1-1.
That goal seems to have taken the competitive edge out of the game, and it’s all gone a bit flat here in Mendel’s garden. A few missed passes and long waits for the ball to be retrieved from behind the pea plants are making everyone feel that November cold and start thinking about the after-match hot chocolate.
But wait – Greg Laden has the ball again! The man from Minnesota is making maneuvers and heading for goal. Ohhhh, but he got distracted by some birds messing about in the pea plants. Avian adulterers might go for the best-looking mates, but that’s no excuse for taking your eyes off the ball.
Luckily for Greg’s team, Mendel picks up the ball in midfield (midgarden?) and gives us another glimpse of that magic footwork. He’s round Matt, he’s round Wenchy, he’s bearing down on an open goal… but if I stretch and put in a sliding tackle, I can juuuuust put a toe on it… the ball careens off, Mendel goes flying, and ball and monk each take out a whole row of pea plants. Oh no! Decades of work ruined – who’s going to be the father of modern genetics now? – and Mendel’s gone off in a huff. Hey, don’t look at me like that, it was a fair challenge.
Well, if you’re going to be like that, I’m going home. And I’m taking my ball with me. Game over.
Rematch in December at The Inoculated Mind.
The bad news: one third of the world’s primate species are critically endangered.
The good news: a new population of De Brazza’s monkey (pictured) has been found in an unexpected area of Kenya, a country in which the species is rare.
The mixed news: the monkeys have colonised new habitats due to rapid climate change. Good news for this one species, but the wider effects are almost guaranteed to negatively impact other species and ecosystems.
Happy Hallowe’en!
You might think I have a thing for flies, given the subject of a couple of recent posts. Well, you might be right. Here’s me at last year’s Hallowe’en party. Two sieves, some hair elastics, a single black stocking and some coat hangers. Voila – one fly costume. Good stuff.
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That handsome young Wolverine is my lovely new husband by the way.
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Update: more Hallowe’en fun with Bayblab’s grant application
I’ve always tried to cover the most up-to-date research in my journal club series, but today’s paper is an exception. “Strong Selective Sweep Associated with a Transposon Insertion in Drosophila simulans“ was published in 2004, and I actually covered it for my old lab’s journal club when it first came out.
So why am I coming back to this research now?
The answer is that Todd Schlenke and David Begun’s paper is a fantastic illustration of positive selective pressure acting on a beneficial mutation. It is therefore extremely useful when debating creationists, as I found out in the extended comments thread on an older post. (For some reason, fruit fly genetics papers often make good rebuttals to creationist thinking.) Some creationists claim that mutations are always harmful and therefore can’t be used as the basis of natural selection and evolution. They believe that the likelihood of a mutation being beneficial to the organism is practically nil, and that species therefore did not evolve but had to be designed. The evolutionary model proposes that beneficial mutations are indeed rare, but are powerful drivers of natural selection when they do occur.
Are you positive there was selection?
The “selective sweep” of the paper’s title refers to rapid positive selection of a beneficial mutation. That means that the mutation conferred a strong enough advantage that the mutant fly and its offspring reproduced much more successfully than other flies, and the original mutation quickly became the population’s new “normal” sequence. When a mutation spreads rapidly, there is not enough time for the mutated chromosome to exchange segments with its sister, normal, chromosome1, and a block of the original fly’s DNA surrounding the mutation is passed down to all offspring more or less intact.
It is possible to scan the DNA of different members of the same population for blocks of chromosome that show no sign of crossing over. Schlenke and Begun, who are based at the University of California, Davis, performed just such a scan with local fruit flies of the D. simulans species. They found a large chromosomal segment with no evidence of chromosomal exchange on which to focus their studies.
Time flies like an arrow, fruit flies like a mutated regulatory region
There are 22 different genes in the region of interest, and one of them looked particularly interesting. Cyp6g1 codes for a protein that is involved in detoxifying various chemicals, including insecticides. It also has a transposable element (similar to an endogenous retrovirus) inserted in its transcriptional regulatory region. The element is almost identical to the standard sequence for its family, which indicates that it hopped into position recently enough not to have accumulated many mutations. 98% of the flies caught in California possessed the exact same insertion. So this is a recent mutation that has spread extremely rapidly to become the new normal sequence in this particular population. What an excellent candidate for the cause of the selective sweep in this region of the genome.
But what does the insertion do? It must have something to do with the expression of the Cyp6g1 gene, right? Right. Flies with the transposable element expressed higher levels of the detoxifying gene than flies without the mutation, and were slightly more resistant to the notorious DDT insecticide. Another example of the potential evolutionary impact of changes to the regulation of gene expression.
Under pressure
A beneficial mutation will not spread rapidly unless there is some kind of selective pressure acting on it. In this case, the pressure was probably exposure to a toxic chemical of some kind, rendering an increase in Cyp6g1 expression much more useful than it would have been in a less toxic environment. DDT was used extensively in California between 1945 and 1972, but the slight increase in DDT resistance in the mutated flies does not appear to provide enough of an advantage to explain the speed of the selective sweep. In addition, the frequency of the mutation would most likely have fallen in the last 35 years once DDT was removed from the environment. Cyp6g1 provides protection from a range of chemicals, and it is likely that something other than DDT was responsible for the initial rapid spread of the transposable element insertion, and is now responsible for maintaining the high frequency of the insertion in the population.
The proof of the pudding…
The importance of a research paper can be inferred from the number of times it is cited by other authors. The Schlenke-Begun study has been cited an impressive 54 times to date2, by authors who have found their own examples of selective sweeps as well as those who are interested in transposable elements or pesticide resistance. So this paper stands out not just because it’s a neat scientific story that beautifully illustrates a key point in evolutionary theory, but also because of its cross-disciplinary impact on multiple fields of research.
Beat that, creationists!
1This process, known as crossing over, occurs between pairs of identical chromosomes as the sperm or egg cells are produced. Recombination ensures that the chromosome sets you inherited from your mother and from your father are not passed down intact to your own children, but instead swap segments between the two sets to create a unique chromosome sequence in each new individual.
2Bastards. Yes I’m jealous.
Various blogs have picked up on the story about a man being killed by monkeys in India. (Hey guys, primates in the news are my thing. Mine.) So I’m going to tell a different Indian monkey story instead.
newindpress.com reports that a monkey is attacking a herd of piglets. Maybe not so unusual, except that until recently the monkey was in charge of the herd and apparently took excellent care of them. He guarded them from dogs, chaperoned them across roads – not quite a sheep-pig, but a pig-monkey.
The new Tangled Bank is up!
I followed one of the links and discovered a new favourite blog, complete with monkeys, viruses and everything. Hooray for carnivals!
I’m getting a good workout as I gradually clear my desk and locker of all the stuff I’ve accumulated in the last two and a half years. Bags and bags of shoes, text books and all kinds of other stuff are dutifully being loaded onto my bike and hauled up the hill every night.
I’ve never been a tidy person, and my workspace is testament to that.
BUT I want to make a good impression in my new job. So I resolve that:
I have one more week in which to get into good habits in my old job. My desk is decluttering nicely, but it is not helpful that people who hear the big news are prone to greeting me with “Dude! You’re leaving??!! That’s awesome!!”
So last night I dreamed I was back in the lab. I didn’t recognise the room, but some of my old lab mates were there. I was radiolabelling a probe for a Southern blot using my old protocol, which I’d had to fish out from behind a bench of unfamiliar equipment. It’s been more than 2 years since I finished my postdoc.
This always happens to me when I’m close to a big change. I dream about old jobs / classes for a couple of weeks, start the new job, and have normal dreams for a while. Two to three weeks after starting the new job, I will dream about that for several nights in a row. Then I’ll be OK again until the next time I move.
Is this normal?
Commuting really sucks right now – for everyone. It’s raining, it’s getting darker, and there’s still construction everywhere. At least the garbage strike is over, eh?
I have some helpful suggestions for those motorists who choose to avoid the congestion by driving on the city’s designated bike routes.
First of all, please respect the fact that you’re choosing to use what for most of us is the only safe route. (Those “local access only” signs that keep getting knocked down or pushed to the sides of the road are there for a reason.) The favourable stop signs and bike-activated crossing lights on these roads are as convenient for you as they are for us, so I can see why you’d choose to drive on the bike routes, but we don’t really have another choice. I cycled down the main roads (Fraser & Broadway) once after a snowfall, before the bike routes were cleared, and it was terrifying. I take the bus instead now, even though I HATE the bus. So please watch out for bikes (hello to the jackass who pulled out from a parking spot JUST as I was passing him last week), give us space, and don’t honk or act aggressively (e.g. trying to block the gap between the cars and the kerb) when we squeeze past all the cars that now use the bike routes as we try to press the crossing button.
Secondly, please please please learn how to use traffic circles and roundabouts properly. They’re not just a traffic calming measure (like a speed bump), they’re actual road features with actual rules (like a stop sign.) Here’s the official word from ICBC – page 6 onwards. The most important points are:
– ALWAYS go around the circle in a counterclockwise direction (i.e. turn right into the circle.) Yes, even if you’re turning left. Just go 75% of the way around the circle before exiting. I have almost been hit several times by people who look directly at me as I approach the circle, signal left, and then cut across my path.
– Yield to vehicles already in the circle. That includes bikes.
– It would be very helpful indeed if you could signal your intended direction as you approach and enter the circle. I believe some of you have flashing lights on the sides of your vehicles that indicate your intentions to other traffic. Could just be one of those urban legends though.
(A polite word to those of you who let cyclists across first, even when we get there after you or you’re already in the circle. It’s extremely nice of you, and I do appreciate the thought – especially when it’s raining or I’m trying to maintain my momentum up a hill – but ultimately it’s easier and safer for everyone if we all follow the same rules all the time.)
Thirdly, please signal your intentions through your lights, road position and movement, not by hand gestures. Car windshields are very reflective and I can’t always see your face and hands, especially when it’s dark. I also have to keep my eye on all the other vehicles on the road. So if you’re waving me across while you keep inching forwards, I’m going to assume that you’re not stopping. If you come to a complete stop then I know what’s going on and we won’t have to do that frustrating dance when we both lurch forwards at the same time and then both stop.
There are good and bad drivers, just as there are good and bad cyclists. I play by the rules – I respect traffic signals, stop signs, and traffic circles1 and I ride defensively, never aggressively. Overall, cycling in Vancouver is much safer and more pleasant than in Glasgow, where I lived before. There’s room for all of us out there. Please just respect our space, and please, please, please go back to using Cambie when it reopens.
Thank you.
1Most of the time. You know, unless there’s clearly no-one else around.
