ingrid: photo of me (Default)
2011-07-10 04:38 pm

Introduction to experimental human genetic & developmental biology

AKA my experiences of pregnancy, birth, and caring for my child, given my background as a biologist focussed in evolutionary genetics and bioinformatics.

There's so many things to write about: my experiences while pregnant, giving birth, and now dealing with this charming alien living with us. And how Western culture is child-hostile in so many ways. It's hard to decide where to begin, particularly when attempts to write often get interrupted these days...
ingrid: photo of me (Default)
2010-07-25 12:37 pm

Serious philosophy?

I'm not a philosopher, and I've just read an apparently serious article by a philosopher which puts me off ever becoming one.

Seriously, this is an argument? Contemporary philosophers are allowed to spew out that quantity of word salad and still be taken seriously without apparently having given any thought to the subject matter of the word salad? Philosophers are not expected to think sufficiently about their subject matter to determine whether or not it's a binary, yes/no quantity, or just perhaps something with degrees?

And "free will", that philosophical subject of centuries, hasn't been thought about in sufficient depth that it's obvious to philosophers that it in particular isn't a binary, yes/no quantity? So that anyone who assumed that about free will in particular doesn't get laughed out of the academy immediately?

So, instead of any kind of interesting discussion about how one might develop more and more free will as one grows from a newborn into adulthood, and how particular decisions at particular points in time might make it easier or more difficult to develop one's abilities in terms of making moral decisions or taking responsibility for actions, and perhaps an excursion into the extent various animals might have some degree of free will, we get a beating-over-the-head with a paradox that doesn't remotely look like one to me?

I am quite happy to stay an evolutionary biologist, thanks.

Far more interesting stuff that grabbed my attention this week: solar-powered flying craft stays up for over a fortnight, so it's clearly collecting enough energy during the day for not just daytime flight, but to charge the batteries for nighttime flight.

Prion protein mutation that causes a structural difference that gets us closer to understanding what's going on with prion diseases.

Again off in my particular area of interest: another example of plentiful recombination and gene conversion in this case between strains of Streptococcus and including housekeeping genes.

On the other hand, divergent sheep DRA allele that's not undergoing much recombination.
ingrid: photo of me (Default)
2010-05-22 11:12 am

Sciencey linkspam

Of course everyone is talking about Craig Venter's synthetic life, but I'm rather blasé about it because I'm sure I heard about completion of the synthesis of the genome some months ago, and they already had the technology to insert genomes into hosts. And the genome is synthetic in the sense that it was synthesised base by painful base by commercial equipment, but the sequence is based on another existing species.

It might be important to some people that the DNA was sequenced on a machine rather than duplicated from an existing organism's DNA, but biologically it (of course) makes not a scrap of difference and so it's not a big deal from that point of view. I guess it can be compared to the first synthesis of urea; but I thought that had already established that life consists of the same chemicals non-life is made of. Those of us who've worked in molecular biology labs know that no-one keeps track of whether particular DNA is of biological origin, duplicated in the lab using polymerases, or comes off a synthesising machine, except in terms of budgeting. Synthesis is expensive.

I do find it amusing that several genes are non-functional because of errors during construction of the genome. The high quality of DNA synthesis in vivo is enforced by natural selection - if there are too many errors, the organism won't survive in the wild. And yet some people persist in weird terminological arguments that evolution can't work because selection requires someone to do the selecting.

I thought the walking fish are much more interesting and make for better pictures:
The Pink Handfish is known from only four specimens and was last recorded off the Tasman Peninsula in 1999.
Image credit – Karen Gowlett-Holmes

The Zeibell's handfish is restricted to isolated populations off eastern and southern Tasmania.
Image credit – Andrew Maver

spotted walking fish
Image credit – Phil Malin

Let me do some Completely Serious Adult Scientist squeeing about their little handsies. Gosh, they are cute. And it makes it much easier to imagine that whole "fish dragging themselves onto land" scenario when there are fish dragging themselves around on the ocean bottom.

Anyone who likes to hang on to their human uniqueness has lost another point: Yes, chimpanzees are more likely to follow the example of a high-status individual. It's well-embedded in us to not just care about information, but the source and authority of that information. Of course in many cases "high-status" doesn't mean squat about actual authoritativeness, but I suspect that's largely a complication introduced by the higher complexity of our societies and knowledge.

I need to read this in more detail to see if I think what they're doing is useful, but the problem, of combining a variety of free-text data relating to species and classification, is certainly real. If I was still working on skeletal ontologies, I'd have read it by now.

And harking back to my PhD, large-scale cheap HLA typing of East African populations. It's interesting that they think a requirement for cheap typing is focussing on the specific alleles expected in a particular population - I guess cosmopolitan populations with their diverse genetics are always going to be messy.
ingrid: photo of me (Default)
2010-04-11 02:00 pm

Busy weekend

It's been a pretty busy weekend for me so far. I think I get to relax a bit now.

Yesterday morning, the bike bridge/path between Kooringal Drive and Mt Ommaney Drive was officially opened. We walked over there and arrived too late for the free sausages but did get a free coffee (James) and hot chocolate (me), stared in amazement at all the people, got some bike maps, talked to Ben and Bill from Bicycle Queensland, and of course walked on and admired the bridge itself.

It has turned out to be an expensive affair, it's the longest single-span aluminium bridge in Australia, but the upside of that is that the creek, the sides of the creek, and the vegetation along the creek has been left alone. In fact, the bridge is a good up-in-the-trees vantage point if you're a bird watcher.

Then in the afternoon, Annette and I headed to Ipswich for the official opening of The Fabric of Society: Australia's Quilt Heritages. Annette had got an invitation because a quilt made by her great-aunt is in the show. Annette Gero gave an interesting talk about Australian quilt history - quilts were made by convicts on the ships heading to Australia, and there's two quilts now suspected of being from that era. Australia also has a number of other very old quilts because govenor's wives brought out family pieces, and later migrants similarly took quilts with them, which they then kept particularly good care of as their old-world heritage.

A number of the quilts are from Australia's prosperous colonial period - the fashionable crazy quilts made of velvets and silks, decorated with intricate embroidery (I had no idea variagated embroidery thread was available in the 1880s, but that's what a lot of the quilts from that era seem to be using), log cabins in rich silks, and a grandmother's flower garden where the hexagons are penny-sized, fussy-cut around tiny flowers printed on the fabric, and the entire quilt - single-bed sized - awe-inspiring in the amount of different fabrics and sewing time required.

But the truly Australian quilt form is probably the Wagga (including Annette's great-aunt's quilt). These were originally made from used flour sacs, wadded with newspaper, as blankets by people who literally could not afford better blankets. They came to be made of the good parts of worn-out suits, and tailor's fabric samples. Annette's great-aunt worked as a tailor, so had ready access to the fabrics - I suspect some parts of her quilts were offcuts from re-fitted suits. One quilt in the exhibition was made from furnishing fabric samples.

Australia went through a depression in the 1890s, then there was World War I, the great depression, WWII. A lot of people were struggling to get by, for quite a long time. And because these were hard-times quilts, and Australians don't understand how their quilt heritage differs from the more famous American quilt heritage, these quilts are mostly still in the possession of the families in which they were made, and so come with a lot of family history. Annette could share her memories of how this quilt would come out when she (or one of her brothers) was sick, and now it's on a gallery wall.

The Wagga seems to have been made by both women and men, based on need, and Australian men have their own quilt genre - the decorated army blanket. Dr Gero showed pictures of the most astounding example of the genre, by C.A. Gatenby, a soldier who was a prisoner-of-war of the Germans during WWII. He embroidered the blanket with scenes of places he'd served, the prison camp both in summer and winter, maps of Australia and various Australian animals. It now finally hangs in the Australian War Memorial, as it deserves. But in the exhibition was a somewhat more quilt-like example, where a soldier had covered his blanket with his unit's patches - all the leftovers that hadn't been used at the end of the war.

This morning I went to bushcare at Jindalee Creek, riding my bike over the new bridge of course! I thought I was going to get a blister from shovelling mulch, but I got a blister pulling out weeds instead. When I'd finally worked across the bottom of my patch (Rod: "I hope you don't mind, I'm thinking of that (gesturing) as your patch" Me: "I was working on the same assumption" - I've been down there pulling out weeds every time I've been there, only three times so far admittedly, but the pattern is well-established now) and stood up, I discovered my entire front, down past my knees, was soaked in sweat. I think I worked enough.

I still have some bananas to turn into banana bread and some meat into curry. That'll be enough weekend for me.
ingrid: photo of me (Default)
2010-04-05 10:35 am

Internet censorship

Dear Senator Conroy,

Stop being so embarrassingly out of touch with your own portfolio. Lee Kuan Yew, "minister mentor" of Singapore, a control freak extraordinaire, understands the practicalities of the internet better than you do. From The Singapore Solution by Marc Jacobson (that is weird for me to type!) in the January 2010 issue of National Geographic:

The great engine of cultural change, of course, is the Internet, that cyber fly in the authoritarian ointment. Lee acknowledges the threat. "We banned Playboy in the sixties, and it is still banned, that's true, but now, with the Internet, you get much more than you ever could from Playboy." Allowing pornography sites while banning magazines may seem contradictory. But attempting to censor the Internet, as has been tried in China, would be pointless, Lee says. It is an exquisitely pragmatic reply. [p.148]

If Lee Kuan Yew, who is significantly older than Conroy, and has much broader political interests and responsibilities, understands that the Internet is not just another medium that can be controlled like magazines, the fact that Conroy can't, or won't, speaks volumes about either his comprehension or his motivation.