Thursday, October 28, 2010

Tuesday, October 26, 2010

Too cute! My kind of cute Part II

By the amazing Nick, via here.  There are more - and more amazing.  Whoop!

Must be done by laser, surely

Egg carving - impossibly amazing.
egg carved,egg sculptures
egg carved,egg sculptures
egg carved,egg sculptures
egg carved,egg sculptures
egg carved,egg sculptures
How could you bear to touch them for fear of breakage by your buttery monkey fists?!

Labourious Labour Weekend

My flatmates have started a wee vege garden:
You'll note the Trouble-proof fencing, which, so far, has indeed proven to be Trouble-proof.

Of course, I went about a week before I wanted to have a go - never one to be willing to miss out, and occasionally I do like being in the garden (as opposed to just sitting in the garden reading...or drinking) - and more often that not I love getting my hands dirty.

So I dug out, fenced off, dug in (fert and compost: yummy!) and planted dwarf beans, silverbeat, cauli, broccoli and butter crunch lettuce.

So far the fence has kept Trouble out (between turning the soil and digging in the compost I found 3 bones he had opportunistically buried, I'm pretty sure he went around digging them up to re-bury them in the fresh soil, the little shit), but now I just have to wait and see if anything grows.




Not my best strength.

Friday, October 22, 2010

Photos that make me want to cry Part IIX

Nikon Small World Competition.


Some of my favs:

And the bestest (not actually my super-fav, but I feel pressured into being fly-girl.  I blame society):

Just brilliant.

End of an Error?

It's happening.

I don't know what to feel - there will be massive loss, and bad; but potential for good and improvement

To be honest, you could see it coming - students are of such a different ilk these days (yeah, I am that old).  The political awareness had gone - as has the clout; the caring about what is happening outside of their own narrow lives is non-existent, and the demand for services from their Students Association is limited to boozy Orientation events.

This move will shift the Association in line with current student opinion, wants and apathy - whilst removing the supposed support from minority groups who constantly stack Student General Meetings to swing votes in their favour - passing motions supposedly supported by the majority of the student population.  (think about ~200 students needed at a meeting for quorum, representing ~20,000 students in total - and a majority vote from those 200 present to pass a student-body-wide support vote for campus public smoking of weed, to highlight a specific contentious example).

In the spirit of full-disclosure, I served on the Otago University Students' Association Board of Executives as Science Divisional Representative for the 2008 academic year- so I am aware of the issues, the challenges, the good and the bad.  I both loved the association and all it was trying to achieve, against all odds - and also got amazingly frustrated at the internal politics, the inefficiency, in-fighting, ancient policies and traditional expectations.

I just cannot decide how to feel.  This is the end of an Era, but potentially the end of an Error also.  Students Associations have been steadily loosing contact with their electing body - students no longer care about the same issues that made the associations so successful and essential back in the day.  Marching for equal rights, protesting fee increases (though the need for it has not diminished), meeting to debate politics or the local body elections, membership in 'young xxx' political party groups, club and community involvement etc etc.  Even getting anyone to vote in the new Exec is a struggle, let alone encouraging students to participate in the local body or governmental elections.

Lets blame the Sham factory again.  The increasingly immature freshers and the general student-wide apathy.  The advertising of universities as a right of passage, the expectation of a irresponsible and dangerous social life, the allowable trashing of property and city - which is then left behind as the student moves back up North after three short years, passing papers with minimal effort and C's across the board.

Wow.  Hold me back.

I will mourn for the past, a little - and for the lost opportunities.  The potential still exists for Students Associations to make an impact, if they could re-invent the system, and the experiences I gained that year could never be replicated in another context.  I loved all the good parts - being involved with the student body, working with the university on committees and such with a student opinion, the different (different) people, the brilliant permanent staff, having my eyes opened to such a new world - getting enthused and educated about politics and issues.  So much good - tempered with a more-than-healthy dose of complete exasperation.  But few students will be able to have this experience, with complete autonomy from the University, if when the bill gets passed.

I'm sure the body will remain in some form or another - the facilities and such would have to be absorbed by the university itself, and it will be lucky to have them.  Student support, Clubs & Societies, Orientation Events and so on.  Perhaps a new student magazine will be developed - and replace the box of rat turd the Critic has turned into over the last couple of years.  A new level of professionalism, and a larger, steadier pool of resources.

I guess we'll just have to wait and see.

I almost pee'd a little with laughter.

Make sure your sound is on, people.

Just brilliant.

Thursday, October 14, 2010

Oh yeah, it did

Today just got awesome.

There is a new dinosaur.

There is a new dinosaur, called Sarahsaurus.
Artists rendition of Sarahsaurus, by John Maisano.

You have no idea how excited I am right now.  The paper is in the Proceedings of the Royal Society, Biological Sciences and everybody is writing about it, thought at this point a lot of it reads exactly like the University of Texas at Austin's press release.  It even made Nature Research Highlights - Ooooooooo.

Some stuff about migration is thrown in - waiting for animals to move out of an area before moving in, as opposed to barging in and kicking them out, and evolution of size - that perhaps the sauropodmorphs started off small and then got bigger. (The sauropods (a descendant) are the largest land animals in history)

A beautiful diagram of Sarahsaurus bones, from the paper.

I'm loving the open-ended questions, particularly about the hands:

"Its hand is smaller than my hand, but if you line the base of the thumbs up, this small hand is much more powerfully built than my hand and it has these big claws. It's a very strange animal. It's doing something with its hands that involved great strength and power, but we don't know what."

That's Tim Rowe, professor of paleontology at The University of Texas at Austin's Jackson School of Geosciences, one of 3 authors on the paper.

This beauty is named after Sarah Butler, whom Tim promised to name a dinosaur after if she managed to raise a mill for the Dino Pit.  She did - and he did.  I like it.

On a depressing note - he found it in 1997Thirteen years to publication.  Dedication much?!  Gosh.

Some facts:

Lived during the late Jurassic (190 mil years ago), ate plants, and was about 4.3 meters long and 113.4kgs heavy.

"What makes the amusingly named Sarahsaurus stand out is that this prosauropod possessed unusually strong, muscular hands capped by prominent claws, the kind of adaptation you'd expect to see in a ravenous theropod rather than a gentle plant-eater"

Thanks Bob.  I ravenously love it.  Ha.

"Help me! Help meeee!"

Have been working on my costume for Haloween this week - think Tritovore meets Brundle-Fly less SFX studio.

Like a true MacGyver Kiwi all I had was a bucket, news paper, PVA, poster paints, pipe cleaners - and a truckload of glitter.  (so really, everything I needed. Ha.)

Once again I was so into the project I failed to take photos of the inbetweens, so you will have to make do with the finished product.  (It scares the dog, what more could I need?  On a side note - said dog kept stealing my brushes and paint-water - he will be shitting glitter for a week.)

And my baking-fed model:

Yes, my camera is complete shit.  Yes one eye is longer than the other, and no - it is not scientifically accurate.  Give a girl a break! Sheesh!

One of those days

Yesterday sucked bollocks - started the day by smashing my lip into the window sill - turned away from the mirror to sneeze (no one likes snot on the mirror to start their day) and head planted into the window - only it was open, so just my bottom lip.  Spat out some blood and stood gripping the towel rail for about 2 minutes while my eyes watered and I thought my lip was going to pop off. 

Figure 1. My enemy.

Then we went up Signall hill to collect bumblebees (wanting to harvest their ovaries) and not a one was caught - plus walking back up the BMX track, surrounded by gorse flowers I had my first asthma attack in years.  Years.  Of course my inhalers were all back at work, but somehow I survived with only mortal embarrassment, and lungs that feel like they have been cheese grated.  It will take a couple of days before I can take a deep breath without pain.

Figure 2.  Shove this up and down your lungs a couple of times and see how well you feel the next day.

So not OK.  Hopefully today is an easy one. (Ha! what are the odds?!)

Wednesday, October 13, 2010

I absolutely do not approve

Te Papa is telling women who are menstruating or pregnant that they should not go on a particular behind-the-sceens exhibit tour.  This comment from Helenalex on the Dim-Post feed sums up the situation nicely:

"I find it quite annoying the way they’re presenting this as being for our own good. If they’re actually concerned about spiritual damage to patrons they could say something along the lines of ‘the traditional belief is that pregnant or menstruating women could be harmed by going near these objects; women who don’t feel safe because of this can take the tour at another time’. But instead they are discouraging all pregnant and menstruating women, even those who don’t believe in any of it.
The problem for Te Papa, obviously, is that if they came right out and said ‘pregnant and menstruating women should stay away because their presence would be offensive in Maori culture’ they would be subjected to even more of a shit storm than they are going to experience anyway. But at least it would be more honest."

True - much more honest.  I am a bit surprised, surely they saw the clusterfuck heading their way when they issued such a statement, or made widely public a practice that has been, apparently, long held?!
My athieism extends in all directions (of course) and I do not find the need to exclude Maori belief systems just to "respect their culture".  I respect it as much as I do all other faiths (that is avoiding overt ridicule in their own places; churches, temples, marae etc, and recognising the positive aspects of having a community organised) but I still find facets of it completely hideous.

Like banning a woman from the beach, garden and kitchen because she is unclean.  Thank you Margaret Mutu for holding us back a couple of hundred years by showing us you still think like this.

"Margaret Mutu, head of Maori Studies at Auckland University, said women should not be offended by the request.
"The reproduction area is extremely powerful and can do damage to things that are not tapu. It's about the power of women, not about stopping them."
Mutu said the objects were obviously dangerous and the hapu they came from would have told the museum about how to treat them.
"They are tapu and pregnant or menstruating women are tapu. It would be very unwise to put the two up against each other."
Mutu said in her hapu, women were also prevented from going onto gardens or fishing areas while tapu."

There is a lot of coverage of this 'event', Stuff of course, the Herald, Fark, feminist bloggers, local bloggers, skeptics, and Expats.

On the other side, I liked this piece by Elpie here and liked her points until this:

"For me, I felt a strong calling that was as much physical as spiritual. After voicing this, I was able to visit and pay my respects to the part of the collection that had specific meaning to my iwi. For someone who was not raised amongst Māori culture, what I felt there was both unexpected and powerful. Some taonga repelled me, as though there was a physical barrier I could not see. Others pulled me in. One attracted me so strongly and when I was given permission to hold it, I swear I felt hands holding mine. Fanciful? It probably seems so to anyone who has not had a similar experience around taonga of great power."

aaaaaaaaaaaaaaaaaaaad SMACK.  That was my opinion of you hitting the floor.  Sorry.  Still, if you have to read one piece, make it that one.

For a final soundbite or four, from Jez who has written my favourite piece on the subject:

"Protecting cultures is generally awesome, but you can end up catching all the little crap from a particular era, like flash-freezing a dinosaur when it's taking a crap"

"Telling women they shouldn't do X Y and Z because it's about "protecting them" really puts the patriarchy into patronising."

"they are propagating a piece of - to be frank - superstitious bullcrap under the important umbrella banner of cultural values. Cultural sharing and caring is very important, but in a national museum you really do need a filter for the bullcrap."

"Things like this are not inseparable from the rest of Maori culture - it's not all or nothing. I'd deride anyone for believing in ghosts or spirits or pixies or fairies, and I can do that without causing disrespect to whatever culture and background they're from"

Saturday, October 9, 2010

Poetic as shit I tell you. v2

Trouble has been chasing bumblebees and blossom petals, and today - rolling in the blossoms under the tree.

Poetic as shit.
 Just look at that pose:

Friday, October 8, 2010

Breaking flies

I am at the point in my PhD studies where I am ordering pre-made mutant lines of flies from the US to test out some of the results I found early in my research. It is amazing that we can do this – and for so remarkably little expense. There are vast warehouses in the States and elsewhere that hold rows upon rows and shelves galore of different fly mutant lines – populations of flies carrying a mutation in a single gene. This makes things easy for us in that we can completely skip the mutant generation steps of the experiment and simply order online the mutants we require.

This is all well and good – but I am very much a ‘learn by doing’ type of person and my undergraduate studies appear further away every day.

So – a recap. Drosophila mutant generation and identification 101.

The website we order from provides a search box where you can simply type in the name or symbol of the gene in which you want a mutant line, and a page pops up with every line available with that gene affected. The mutants are all listed with delightful codes and links, and appear at first glance to be some sort of mystic language.

Figure 1. Every option for mutant lines in this particular gene. Different ‘shops’, order numbers, and genome description. Figure adapted from FlyBase.

The particular mutant I have ordered for this gene has an entry of its own which shows us its geneotype – with each element a link which directs us to further information about that part.

Figure 2. Partial Stock Centre Record for mutant Drosophila line 18166. Adapted from FlyBase.

The line ‘FlyBase Geneotype’ tells us all we need to know about that line. The first code, ‘w1118’ tells us that the entire line carries the white eyed marker – this is so that you can tell the flies that are carrying the specific gene mutation (with pink to red eyes) from those that are wildtype, or have no extra mutation in their genome (white eyes). The white eyes are caused by a naturally occurring mutation in the white gene, which is responsible for production and distribution of normal pigment in the eye. In mutant flies like this one, the transposon carries a mini-white gene which partially rescues eye colour - only in flies with that transposon inserted into the genome. Fully wild type flies have red eyes and the white eyed gene mutant was one of the first identified when people started using the fruit fly in genetic studies.

Figure 3. Variation in eye colour – the eye at the bottom is a complete knockout of the white gene. By ArrogantScientist .

So: completely red eyed flies (wild type) should not be in my pots at all, since the entire mutant line is in the white eyed background. White eyed flies could be present but will not carry my special gene mutation. Pink/redish eyed flies will have my gene of interest knocked out. Easy! I can see their eye colour without aid of a microscope.

The second code, ‘PBac{RB}Ect4 e03540’, means firstly that the mutant was created with a transposable element ‘PBac[RB]’. A transposable element, or transposon, is a small section of DNA which is capable of moving around the genome – copying itself out of the sequence and then inserting itself in again at another region. PBac{RB} is a synthetic transposon made up from piggyBac (a transposon originally found in moths), a small piece of the white gene, a FRT site, and a splice acceptor site.

Figure 4. piggyBac transposon. Figure adapted from Thibault et al 2004.

The only part of this that we need to understand right now is that the small piece of white gene (mini-white) is enough to restore partial function of the protein and cause pigmentation of the eyes – from white to yellow or even pale pink/red. As discussed above this eye colour is an easy marker for picking out flies containing the gene mutation. The {RB} in the code is simply an identifier for that version of synthetic piggyBac transposon. It does not matter where in the genome the piggyBac jumps in – the mini-white gene will work to restore eye pigmentation no matter what.

As an aside, the FRT site is used to make deletion mutants – if two transposons are inserted in the genome relatively close to one another the two FRT sites can loop together and the fragment of genome in between is cut out. It was initially a segment of a yeast plasmid, and combined with Flp recombinase (an enzyme which facilitates this looping process) is capable of causing deletion mutants. Deletions mutants are when the gene is cut out – not just interrupted.

Figure 5. Diagram of FRT site recombination adapted from Parks et al, 2004.

The next segment of the code, Ect4e03540, tells us where in the genome the transposon (the piggyBac) has inserted itself. The original screen for mutants in Drosophila involved shooting this wee piece of DNA throughout the genome and then growing up fly lines in which one transposon was present in one gene – so you end up with a library of flies, each with a different gene knocked out. When I say ‘knocked out’ I mean normal function of the gene is stopped completely, or inhibited. A big piece of nonsense in the middle of a gene is usually enough to halt its normal function.

The code, e03540, links us to an entry in the online databases, and shows us exactly where this transposon is.

Figure 6. Section of the genome, showing the insertion location of piggyBac in this particular example highlighted yellow. Figure adapted from FlyBase.

The numbers under the hash-crossed line at the top tell us where on the chromosome this is – in number of bases. The ‘3L’ above tells us this is on Chromosome 3, on the L arm. You can see the chromosomes in Drosophila in Figure 7, and locate 3L. As you can see in Figure 6, there are many insertions in the gene Ect4, each represented by a blue triangle. The gene itself is represented by the longer blue bar under the chromosome location line at the top.

Figure 7. By Steven J. Baskauf.

The second-to-last section of the code, /TM6B, tells us that this mutant line is over the balancer chromosome TM6B. Balancer chromosomes are used when two copies of the mutant gene are lethal – the balancer chromosome keeps the mutant copy in the line of flies, and keeps it single copy only. A balancer chromosome is the same as the chromosome it ‘balances’ but has had big chunks of itself turned over or deleted. This stops recombination; a mixing and swapping of genes that occurs when gametes are being made – so that the new generation have a different set of genes and a greater chance at survival should a threat emerge that favours one genetic code over another.

You can see the available balancers in Figure 8, the F, S and T in the codes stand for chromosome the First, Second and Third. (Original right?!) The phenotypic markers in the third column are the physical characteristics we can look out for to identify the flies carrying the balancer. There is no balancer chromosome for the fourth chromosome since it is so small and considered to undergo no recombination anyway.

Figure 8. Drosophila balancer chromosomes. From HoxfulMonsters.

So no mixing and swapping keeps the mutant gene mutant, and then a marker on the balancer keeps it in the line. This involves a bit of effort – you pick out the flies carrying that marker so that they can then breed – you kill any flies that have dropped/lost the balancer chromosome. This ‘marker’ is similar to the white eye/red eye situation – an easily visible phenotype, and is represented in the last section of the code – in this case, Tb1.

The marker on a balancer is always dominant – only one copy is needed to be able to see it manifest as a phenotype. In this particular line, the marker is Tubby – the larvae carrying the balancer chromosome (and thus, the marker) are shorter and fatter than their balancer-less compatriots. Thus you can easily pick out the larvae you want to work with. The balancer chromosomes also contain recessive mutations, which are lethal if there are two copies of them. So you can only have one balancer present in a genome, and you can tell if it is there by looking at the shape of the larvae.

In the end: you have a mutant line of flies that which you can tell carry the balancer by their shape, and which carry the mutation by the colour of their eyes.

Brilliant. Now you can start some experiments!


This post appears in SciBlogs today also.

Thursday, October 7, 2010


(That was my brain exploding.)

I'm loving the mind bending aspect of these 'Postcards from the future' which tie in beautifully with the book I am reading at the mo (mega mind-blow, is brilliant.  Will review as soon as I've finished.). 

The postcards include an explanation, which is spooky in its possibility-for-truth.  They are part of an exhibition showing at the Museum of London.  Go have a look and read all the captions.  Maybe they will blow your mind too.

London flooded:
"London has become uninhabitable. Every year spring tides surge through the Thames Barrier, making London the new Venice. But whereas the city of gondolas has come to terms with water, London is overwhelmed.

This image shows the impact of 6-metre flooding, the level required to breach the Thames Barrier."

"The climate refugee crisis reaches epic proportions. The vast shanty town that stretches across London’s centre leaves historic buildings marooned, including Buckingham Palace.

The Royal family is surrounded in their London home. Everybody is on the move and the flooded city centre is now uninhabitable and empty – apart from the thousands of shanty-dwellers. But should empty buildings and land be opened up to climate refugees?"

And my favourite:

"London’s busiest urban hub becomes a haven of calm as water levels rise ever higher. Water lilies, fish and wind turbines drift quietly in the breeze, amid empty buildings which are only left standing to support the infrastructure of power generation. Civilisation as we know it has gone."
Via HotTopic and the Telegraph.

Photos that make me want to cry Part VII

From the Cencus of Marine Life
 A picture of Niel Bruce, of the Museum of Tropical Queensland, studying specimens in lighted aquarium on Lizard Island Reef in an undated picture.

   Picture of a siphonophore-- one of the best photos from the Census of Marine Life, which concluded Monday after finding more than 6,000 new species.

 Picture of a poisonous sea slug -- one of the best photos from the Census of Marine Life, which concluded Monday after finding more than 6,000 new species.

Picture of a squidworm -- one of the best photos from the Census of Marine Life, which concluded Monday after finding more than 6,000 new species.

Via NatGeo, of course.

Beaut weather = Ice cream Lab mish

Yesterday was beautiful and hot, so instead of coffee we went for icecream, and I got sprinkles.

I squee'd all the way home, licking the sprinkles off my wee icecream, like an over excited little girl.

Sprinkles, people. Sprinkles.

It was like this - only smaller, and better.