End of Year One

This is just about it from me: we’ve survived the zombies for an entire year, sometimes by the skin of our teeth. We’ve welcomed the founding members of the Science Community of Otago, all 500+ of you (good work on getting in early by the way! We’ve got a linkedIn page, if you’re into that sort of thing), and entranced you with BBQs and quiz night and the rip-roaring Science Ball.

It’s been a good year, if the ever-decreasing amount of sleep I got is anything to go by. Next year should be even better! The President, Secretary, and Treasurer for 2014 have all been chosen by YOU, THE VOTER, and they’re three capable, vibrant young people that will keep improving on the framework that we built in 2013.

The SciCO Exec 2013

From us, the Executive of 2013, it’s mostly goodbye, although a few of the key movers/shakers/cool cats will be sticking around, either on the executive or to lend the occasional helping hand to ensure things run as smoothly as possible. We’ve learned a lot and made a lot of friends.

The Science Community of Otago is a wonderful community of Science Enthusiasts, and I wish you all the best for 2014.

Over and out.

Jet Lag

Hi all, sorry it’s been so long between posts – we’ve been a bit busy, first with the ball, and then with all the upcoming hijinks (Quiz Night Redux, anyone?) – and the exec are in the middle of tying up any loose ends to pave the way for any Excited Young People (that’s you) to come and take the reins for next year. Or, in the case of President, take the reign.

Personally, I (your esteemed secretary, hand of the queen, etc) have been travelling the world and visiting summer; I write to you from Long Beach, L.A., where the temperature is… uh… 80-something. (I gave a talk on the use of scientific concepts in haiku last week at the Haiku North America conference) That’s inspired this post, and the intensive desire to procrastinate my dissertation has made it actually occur. Here we go!

What even is “jet lag”?

Okay, so you know when you travel to England, and it’s really exciting, and you can’t wait to get up early each morning and like, drink tea? But then you can’t fall asleep at the right time, and you can’t get up at the right time, and nothing makes sense and they don’t even have real coffee there? Jet Lag is what happens when you travel really fast, across a bunch of different time zones, so the time zone your body is in doesn’t match the time zone your body thinks it is in.

Source: telegraph.co.uk

That occurs because we developed the technology to time travel (basically). By travelling from east to west, or west to east, you move along a “day” at a speed different to how the “day” actually passes. So, for example, on my flight to L.A., we left at half past ten in the evening, flew for eleven hours, and landed at half past two in the afternoon on the same day. There is no way you can add that up to make sense, and you end up being out by about five hours – which is the time difference between L.A. and New Zealand.

This meant that waking up was the worst, but I wasn’t getting to sleep until midnight or one in the morning, because I was running on New Zealand time. The fact that planes are terrible doesn’t help jet lag, but you’re pretty unlikely to get jet lagged if you fly within the same time zone – you might feel terrible if you don’t sleep for two days, but you won’t be jet lagged!

What can I do about it?

Seeing as jet lag has negative side effects (1,2) including increased mortality in mice (1) and some spatial cognitive defects (2), yeah, something should be done. Melatonin has been suggested to help out with re-setting your schedule, and appears to do so – it works particularly well when done in combination with timed light exposure – most experiments have been done using light boxes, or dorky goggles with bright lights inside them, however wearing dark glasses to avoid unwanted light is probably your best bet (3).

Using stimulants or sleeping pills can also be done, in order to force your body clock into the “right” time zone – sleeping pills definitely send you to sleep, but it is undetermined whether you’re then more awake during the day. What does work (and I am very grateful to know this) is that drinking more coffee not ONLY makes you more awake during the day, but ALSO helps you get over jetlag faster (3).

Go forth and travel widely, but do not forget the coffee!

 

References:

1. Davidson AJ, Sellix MT, Daniel J, Yamazaki S, Menaker M, Block GD (2006) “Chronic Jet-Lag Increases Mortality in Aged Mice” Curr Biol. 16(21): 914-916
2. Cho, K, (2001) “Chronic ‘jet lag’ produces temporal lobe atrophy and spatial cognitive deficits.” Nature Neuroscience 4: 567-8

Unhealthy Sciences

Yooooo. Is health sciences not your jam? (Is CHEM191 just, the worst?) Are you unsure of what to do now you realized that not studying and instead sleeping 15 hours a day in exam season didn’t pay off? (Or, alternately, you studied really hard, the exam was just harder.)

COME AND TALK TO PEOPLE ABOUT THINGS.

We’ve got some ex-health science first year people coming along to be ASKED QUESTIONS by YOU yes that’s right YOU. Want to know how to go about never going anywhere near chemistry again? I’M PRETTY MUCH AN EXPERT ON THAT.

Or, we have chemistry majors coming as well, and they’re all right too. (and some postgraduate entry students, who can tell you what it’s like to do med after a degree.)

You might have seen and chatted with us at course conf – I know I waxed lyrical to a young lady about the wonders of genetics – but even if you didn’t, come and hang out with old people. Really. I’m 20. That’s practically ancient.

The event is here. It’s on Tuesday night, we’ve got St David’s foyer from 6-9, so just rock along and ask whatever question is bothering your brain.

See you then, my lovely first years!

Books!

You may have noticed that this is not the pre-written oracular spectacular that you usually get posted to your inbox/facebook at 7am on a Sunday morning.

That’s because I’m on holiday.

However, holiday is a relative term, and I have been reading quite the spectacular book – The Genome Generation, by Elizabeth Finkel. It’s a good read, aimed at a ‘vaguely educated’ audience, and also covers a bunch of the 300-level genetics course, so I keep recognizing names that I cited about a million times in assignments last year.

From http://www.cosmosmagazine.com, the cover of the book I’m reading RIGHT NOW.

It tells the story of discovery about many of the facets of DNA, from ancestry, to disease prediction, to GMOs, and is written by an award-winning science journalist (and in my opinion, one of the best science writers out there). I get a little bit fangirly over science writing (can you tell?), but this is legit one of my favourite books, like, ever.

(I quite like The Selfish Gene as well, but you do have to take Richard Dawkins with a grain of salt.)

If your jam is more physics, you can’t do better than Lisa Randall (Warped Passages or Knocking on Heaven’s Door) or, my brother is reading some Feynman right now that is apparently quite good although doesn’t beat minecraft out at the end of the day.

Are Angels Ok? is a nice collection of short stories that arose from New Zealand poets/writers collaborating with New Zealand physicists. Some bits, such as the limericks about the nature of light, are certainly hit, and some stories I found perishingly dull, but each to their own (I am a very impatient reader). (Speaking of science poetry, here’s a nice one)

General science books to try are Falling for Science by Bernard Beckett – aimed at a less educated audience but very excited about everything. Bernard Beckett is a New Zealand author as well, which always makes me quite happy. I really enjoyed his book Genesis, a young adult science fiction novel that is also about philosophy, and I enjoyed Jolt to an extent – it was required reading at my high school for some classes (Year 10, I think), which always reflects on a book unfairly.

(I am now quite tempted to go on a rant about how the printing press was developed because YOU GUYS that was SO INCREDIBLY COOL, but I also really want to get back to this book.)

Anyway, there are some reading ideas for the holidays. Go forth and be well-read.

Computing Evolution

Now I’ve discarded that “Spotlight on” jazz, I have to come up with slightly snappy titles, which is kind of annoying. Oh well, today we’re going to be talking about evolutionary trees/trees of life/phylogenetic trees (if you must, but a lot of them are still made without using genetics at all).

Here’s a great example:

Randall Munroe, xkcd.com

The first tree like this was made in 1865. This dude, St George Jackson Mivart, gathered a heap of detail on different primates, and then made a tree showing which were most and least similar. It’s obvious that lemurs are pretty different to orangutans. But when you’re looking at two species of monkey that are both small and adorable, it’s kind of difficult to know which one was made into a pet by Justin Beiber, and which one… well, was lucky.

So St George Jackson Mivart made a tree separating primates on their spinal columns. Cool, a relationship between these species. He then made another tree, separating primates based on their limbs… and got a different tree.

Obviously this wasn’t an ideal situation, and things haven’t improved much.

Several species of stick insects - can YOU make a phylogenetic tree from them? (2)

Several species of stick insects – can YOU make a phylogenetic tree from them? (2)

Today, DNA is taken as the gold standard, because it shows changes that might not be physically seen. Different genes show different relationships, and while one study might use a particular gene to determine where on a tree an organism is, another gene might show something completely different.

As it turns out, another gene does show something completely different, basically all of the time (1).

Because of this, the dudes that did that study, Salichos and Rokas, developed an algorithm to check which bits of the “tree of life” (although in this case, more of a “tree of yeast”) were legit. This now allows really good (informative) genes to be selected with which to build these trees. (I kind of want to go on a rant about how this is a great example of singular value decomposition, but that’s really just exams talking.)

The thing is, sometimes people prune their trees really strangely. If you pick the wrong gene (or the wrong trait) to look at, then you’ll get really funky results. If you’re looking at the ability to open jars as a trait, we’re really closely related to octopuses (octopodes, if you will), but not so much to most mammals. But if you look at, say, having internal thermoregulation (“warm-blooded”), making milk for our young, giving birth to live young, being covered in hair, and having five digits at the end of each limb, then you come up with a tree that makes us most like other primates, similar to mammals, and not very much like octopodes.

Photograph by Nick Hobgood, from en.wikipedia.org

The thing is, most of the time we don’t need all the information about random genes that everything has and there’s a little bit of divergence in. We’ve all got genes for ribosomes, and DNA polymerase, and that other really important junk your cells need to divide, but chance can make those genes in us look more like those genes in a cactus (pl: cacti), or a platypus (pl: platypus) than in a chimpanzee or bonobo.

It’s way better to look at things that actually inform on whether humans are more like cacti than capuchins, and that’s what these dudes have done, using some sweet computational algorithms and a large amount of yeast.

 

References:

1. Salichos and Rokas (2013) “Inferring ancient divergences requires genes with strong phylogenetic signals.” Nature doi:10.1038/nature12130

2.  Buckley TR, Attanayake D, Bradler S. (2009) Extreme convergence in stick insect evolution: phylogenetic placement of the Lord Howe Island tree lobster. Proceedings of the Royal Society, Biological Sciences. 276: 1055-1062

Tutankhamun

Ever since I was very small, I had this huge passion for ancient Egypt. It seemed like such a mystical land, full of danger and wonders and adventure. Mummies were this insight into a bygone era – admittedly an insight into the 1% of the bygone era, but they were just like us.

Rameses V got smallpox, just like we would if smallpox was around today. The pharaohs carved their heads into cliffs before it was cool. They liked gold (we like gold!). Hatshepsut was an incredible badass (“Women can’t be pharaohs  Oh look I’m wearing a beard, I must be a dude.”). And so on.

Photo by Bjørn Christian Tørrissen, source wikipedia.org

But everyone’s favourite has always been Tutankhamun. The boy-king, who ruled from ages 8 to 18, whose tomb was discovered by accident by Howard Carter and Lord Carnvarnon in the 1920s. We did SCIENCE on Tutankhamun in 2005, using a CT scan and modern forensic knowledge to investigate what killed him.

Tutankhamun’s death has been the source of speculation for some time, and it has been suggested he was assassinated. Tutankhamun’s tomb wasn’t as large as a pharoh’s should be, and his coffin had been manhandled quite a bit. The investigations in 2005 showed no significant signs of foul play, but the scan did show a badly broken leg.

Due to the predilection of the Egyptian royal families for incest, the idea that Tutankhamun had some form of a genetic disease is one that has been tossed around for some time.In 2010, a group of researchers performed an exhaustive study linking ancient DNA obtained from all the mummies within Tutankhamun’s tomb both to physical aspects, and what might have occurred back in antiquity (National Geographic) (1).

What do we know now?

Well, “know” is a bit of a strong word. We’re more certain that everyone, ever, always was related (not a huge surprise; in order to prevent dilution of the blood line, brothers married sisters a whole bunch).

It became more clear that Tutankhamun had a deformed left foot, perhaps explaining why he was so frail (as moving around would have been super painful), and there was some DNA from the malaria parasite amplified. That might suggest a combination of factors leading to Tutankhamun’s death, from the broken leg, potential infection, and co-infection with malaria; it’s something a modern-day person would have difficulty with, and we have quinine (an anti-malarial agent, found in small amounts in tonic water).

However, ancient DNA is a tricky beast, and all our methods are pretty biased towards modern DNA, and these are mummies that have been handled by a lot of people since 1920.

The fact that this information wasn’t a surprise gives some credibility to the findings, but it’s super important in ancient DNA analyses that you say every single thing you did to make sure your results were right; Hawass et al didn’t, so they got criticized a wee bit (2). Plus, there’s a bunch of evidence that suggests Egyptian mummies *shouldn’t* have DNA in them (3).

And let’s not even start on how it totally turns out that Hawass is the Hawass, the diva that revolutionized Egyptology and is so embroiled in politics in the way we totally pretend scientists aren’t. (And he has his own clothing line).

A publicity shot from the Zahi Hawass clothing line. Egyptology doesn’t have to look like anything except Indiana Jones, with Hawass.

References:

1.Hawass Z, YZ Gad, S Ismail, R Khairat, D Fathalla, N Hasan, A Ahmed, H Elleithy, M Ball, F Gaballah, S Wasef, M Fateen, H Amer, P Gostner, A Selim, A Zink, CM Pusch  (2010) Ancestry and Pathology in King Tutankhamun’s Family Jama-J Am  Med Assoc 303(7): 638-647

2. Lorenzen, ED, E Willerslev (2010) King Tutankhamun’s Family and Demise Jama-J Am Med Assoc 303(24): 2471

3. Gilbert MT,  Barnes I, Collins MJ, Smith C, Eklund J, Goudsmit J, Poinar H, Cooper A (2003) Long-term survival of ancient DNA in Egypt: response to Zink and Nerlich.  Am J Phys Anthropol. 2005;128(1):110-114