Wednesday, 26 November 2008

Severe Lack of Work Happening

The Gemstone Party was much fun and very pretty. There are photos somewhere, possibly I will show you someday. Everyone seemed to enjoy themselves, the red velvet cake was enjoyed by all who had some and the banana bread wasn't too awful, despite 16 times the amount of bicarbonate of soda.

The Sweet Peas are flowering. So far all the flowers have been a bright, pinky purple. I'm hoping that some of the other buds will mature into flowers of different colours, but quite possibly only one plant is actually flowering at the moment. It's hard to tell them apart.

I'm currently not working on the CMP for Klasies River. I've sent in my November invoice and am wondering when the hell I'm going to find time to do 12.5 hours in December. I'm sure I'll manage it, but given that I was planning to start milling this week it's mucking up my schedule something awful. Currently I am attempting to reformat the bibliography in such a way that it still tells me exactly what I need it to and yet makes sense for the other people who need to read it. [For the record, the wikipedia selection of South African archaeologists is severely lacking. Someone should update it, but that someone isn't me.]
So, how does one compile a bibliography that contains every paper that so much as mentions a particular site? You find yourself a database, do a search and download pdfs of the articles. And then, you scan every single one of them for every single mention of the site and make sure that you make a note of the references it uses, so that you can hunt those down too. I'm quite sick of it, to be perfectly honest, and more than ready to move on to the next phase. But as you may have noticed, I still have a little bit to go...

Tonight we'll be at the Book Lounge for the launch of a new book by Phillip Tobias. After that [or, in fact, in the middle of that], we'll be off to the Opera. Hopefully we'll get to see my darling Patsy with the Orchestra again. As a result of going to the opera, we're missing out on Dystopia's birthday sushi. A sad state of affairs, but somewhat mitigated by the fact that I had sushi on Monday, with theOtherAmy.

Friday, 21 November 2008

All of Nothing

So, today is Friday and tomorrow is the night of the Gemstone Party. I am excited. I'm going to be leaving here early in order to go shopping. In addition to medication, I require ingredients for innumerable baking projects. Not all of which will happen. I also have to decorate. Button plans to work all night, so I can be busy doing other stuff without him getting in the way...

I have [unsurprisingly] a number of Gemstones with which to decorate the walls. My plants are mostly looking fantastic, and some of them are even flowering. I'm extremely pleased with the new plant stand and wouldn't mind a few more. Maybe even a couple for inside. My peace lily has four flowers, with more coming. One of the flowers has opened, the other three are still in pristine white bud state. This is very exciting, as it hasn't flowered since it was first given to us, when Button arrived in the country 3 years ago. Of course, that's in the bedroom, so people might not see it, aside from through the balcony door. And if it's as hot and windless tomorrow night as it was yesterday and so far today, the door will be open. My sweet peas are also set to flower, though all there is to show that is a multitude of buds. I can't wait to see what they look like when they're flowering! My sad nasturtium has once more rallied and has yet another flower about to open. Hopefully the olive tree doesn't get blown over again before the plants have a chance to actually grow.

I've done quite a bit of KR work lately, but not enough for this month. So I guess I'll do that before I go shopping and leave the milling till next week.

Thursday, 20 November 2008

The Stench of Flesh

The THF seems to have done the job. I shall commence freeze-drying later this afternoon, weigh them in the morning and then it'll be back to the milling. The reason that I'm going to start freeze-drying this afternoon, rather than this morning, is that they're going to freeze-dry overnight and I've got to be out of here at around 15:00 today. And there's no reason to have the machine going for quite that length of time. Sadly, the THF doesn't seem to have had much of an effect on Wendell. I suspect he just needs more serious milling.

After the freezer was cleaned out, I seem to have lost what was left of my cow bone. Very sad, particularly since I need some of that cow bone now. So I stopped by PnP yesterday to get some more. I spent the whole of yesterday attempting to deflesh what has turned out to be mostly useless bones, not least because I'm not very good at defleshing. It stinks and the abundance of fat and water resulted in more than a few cuts on my fingers. I guess I should be glad I couldn't find a scalpel and had to use an ordinary knife. Last time I had a femur [a whole one!], this time it's a bit of rib. That's currently defatting. What I need that for, is to test the collagen extraction method we use. When I did my first test of the method [with the original cow bone] the collagen yields were very low, which suggests a need for less severe acid treatment. So I need powder to test that on. So I need to make powder.

In other news, I now have the recipe for Red Velvet Cake, which shall hopefully be made for Saturday. I'm currently in the mood to bake. Probably because I really enjoy doing it and I have space and equipment now. I also have finally taken my recipe book out of my mother's enormous collection and so can actually make more than the few things I have memorised. So, ingredient shopping this afternoon [and tomorrow and Saturday, I suspect].

Why Turnover Rate Matters

Hedges, REM; Clement, JG; Thomas, CDL & O'Connell, TC. 2007. Collagen turnover in the adult femoral mid-shaft: modeled from anthropogenic radiocarbon tracer measurements. American Journal of Physical Anthropology 133:808-816.

* Due to the testing of nuclear weapons, the amount of atmospheric 14C almost doubled in the 1960s and then began to decrease slowly.
* Collagen turnover is important in archaeological science because it affects both the precision of 14C dates and the accuracy of dietary reconstructions.
* Terrestrial food sources have the same ratio of 14C to the other carbon isotopes as the atmosphere, though the signal can take as much as a year to appear.
* d13C and d15N were measured as well as 14C. The d-values for males and females were significantly different.
* Between the ages of 20 and 80 years, the turnover rate of collagen decreases from about 4 to 3%/year for females and from 3 to 1.5%/year for males.
* "Human femoral bone collagen isotopically reflects an individual's diet over a much larger period of time than 10 years, including a substantial portion of collagen synthesised during adolesence."

The reason I'm interested in this paper is precisely because the turnover rate is important in palaeodietary studies, which is what I'm doing. Now that last conclusion, the one I quoted directly is particularly important to me. Our current dietary reconstructions are fairly broad and spotting changes that occurred in later life is particularly difficult. Which is the entire point of my project. If we can separate out the different stages, then those dietary changes should be fairly easy to see.

Shin, JY; O'Connell, TC; Black, S & Hedges, REM. 2004. Differentiating bone osteonal turnover rates by density fractionation: validation using the bomb 14C atmospheric pulse. Radiocarbon 46:853-861.

* Using bone density fractionation [bdf] to separate older, denser bone from yougner, lighter bone.
* The method can be used to remove diagenetically altered bone from archaeological samples.
* Adequate milling is essential for the method's success.
* Results show that the lighter fractions have 14C values that correspond wtih more recent parts of the bomb curve.
* The results were less clear in those individuals that were older at the time of the 14C peak, presumably due to already decreased turnover rates.

The importance of this paper lies in the fact that it's another tantalising glimpse of the method at work. The conclusion drawn by the authors is that bdf does in fact separate the bone into older-denser and younger-lighter fractions. It offers a hint at the conclusions of the paper above, with regard to the slow turnover rates after cessation of growth and the long residence times of bone. Adequate milling might be something to consider in the case of Wendell.

Wednesday, 19 November 2008


So, it's been a few months since my last post. But that's okay. I had a lot of work to be done and blogging wasn't part of that. And, as you might have guessed, the work is actually moving forward! Exciting stuff.

So, the majority of my samples are still defatting. Which doesn't sound much like progress, I'm sure. But it is, and this is why: they are defatting in a different chemical. I was using a chloroform-methanol-water mix. It's a fairly cheap solution and works pretty well. But after 6 months, there was still fat coming out, even with the help of the sonic bath. So, having a look through previous work on this method, I thought it might be worth trying something stronger. The chemical in question is a lot nastier than the solution I was using. But it works oh so much quicker. Chemical nasty in question: tetrahydrofuran. So, while getting chloroform on the skin is annoying, getting THF on the skin is dangerous. Cue lab coat and gloves. I don't object to the lab coat so much, but the gloves annoy the hell out of me. Also, be careful of spilling THF, because it makes the beakers stick to the fume hood.
The reason why this is progress, is because the fat appears to have disappeared. Now one could possibly make the argument that this is because I wouldn't be able to see the fat if you hit me over the head with it. You could also suggest that it's because the THF evaporates so quickly I'm yet to actually change the solution properly. I prefer to think it's because the fat is finally out. I'm going to check on it later today and hopefully I'll be able to start milling later this week [like tomorrow]!

For the rest of today, I should probably work on other MSc related things. But it's getting close to the end of November and I have done very little work on the Klasies River Conservation Management Project. So, I'll probably get to that, once I see it sieving Wendell with THF makes any difference. Hopefully it doesn't make enormous holes in my sieves.

Yesterday, I was at the museum, attempting to find canids for a researcher from the US. She's doing ancient DNA stuff, and is hoping to look at samples from Nelson Bay Cave (NBC) and Boomplaas (BPA). I've pulled out the NBC samples, but I couldn't find the BPA stuff in the store. There were only three boxes of identifiable bone. So, being the bright spark that I am, I hung around and waited for Tyler to get to his office. He did, indeed have the BPA boxes. He was not particularly thrilled to find out that he'd missed three boxes. He's going through and measuring and doing whatever else faunal analysts do to the BPA material. So once he's had a look at the canids, I can prepare them for shipping to the US.

And now, back to work.