Monday, February 28, 2011

Monday poem

I'm not terribly happy with this week's bus ticket, though it does have the right number of lines and that counts for something somewhere. Started off with a neat idea, but the writing never gelled as it usually does between weekend errands. The weekend is up! Time ante up or pass. Catch the Bus here!

Family Photo
On his way to join the circus
Passing through, stopped for biscuits
Truant of the village, old Jim
Out raiding rubbish, caught again
Directing the house justly a princess
Little Clara, future prime ministress
Fighter pilot, police chief, astronaut
Shopkeeper not on the list yet, but...
Sardines, soft cushions, saucers of milk
Being petted by children is not too much work
New house new school new parents again
Life is all change for the orphan
Baths schoolbooks dinners and laundry
She loves them all, especially on Sunday.

Sunday, February 27, 2011

And they're off!

Here it is, the First Blossom of Spring.
An apricot!
The tree is just covered with buds, and next weekend will be robed in white flowers. We'll have to get very, very lucky, however, for these all to become fruit. Never a month of March without a nice hard freeze or several, and perhaps another inch of snow.
The apples, wiser, are not even thinking of opening up yet.

Friday, February 25, 2011

The Doctor is on!

Doctor who?
Not House, certainly. Blue-eyed blech.
Doctor who, then?
Yes indeed! The good, changing Doctor from Gallifrey.
I was a big Doctor Who fan in high school and college. K9! My own K9 unit, that would have been great. I knew a guy who made one out of cardboard and rollerskates. Another friend learned to knit just to make a Tom Baker scarf. He kept going until it was 15 feet long and I taught him finally to cast off. We were a Doctor Who gang: with reruns daily, I think we knew every line of dialog and every continuity error in the Tom Baker-Peter Davison era.
The guy that came after Davison we didn’t like so well, and I graduated anyway and had less time to watch tv. Plus I moved to places where the scheduling just wasn’t convenient, and from there to no scheduling at all.
Just a month ago the new series came to a channel I don’t have to pay extra for, and a time slot I don’t have to record.
Who are these people? Season five already!
Matt Smith? Karen Gillan?
Daleks in happy colors! How can Daleks have happy colors??? It just isn’t right!
And what have they done to the Tardis control room? What is all that stuff? The coatrack is still there. Faithful old coatrack. And the cheesy special effects and ordinary locations. I love it they haven’t gone big-budget like American shows, but have stuck with glue & spraypaint and a bit of quick carpentry.
I must get one of these!

Tuesday, February 22, 2011

ABC Wednesday: F

F is for Forbidden.
It is Forbidden to photograph the huge military monument that dominates the skyline in Algiers.
Not that it’s anything special.
Imagine on top of one of the buttes overlooking the port, a park with a large flat concrete area at the edge. Rising from this is a sort of teepee, three long white concrete arcs leaning in against each other, three or four stories tall. There are no statues of heros or military leaders, only real military guys patrolling with their guns. A few visitors stroll across the vast empty space in the shadow of the monument.
It’s nothing special, not particularly inspiring, doesn’t recall any particular event.
Just don’t whip out your camera for a shot of the thing, with the city laid out below, and the ships coming into port from the hazy blue sea. Whipping out that camera and raising it to your face to frame the best shot of this panorama will certainly get the attention of the military guys. Who are just looking for something to do. Who are coming over to talk to you with their large guns ready.
It’s a good thing then that you have your passport on hand, and your visa, and the letter from the head of the institute you’re visiting, and in fact the head of the institute is right there showing you the sights of Algiers, including this wonderful monument you think is so beautiful and impressive. It’s not quite so good for your passport to be American, but your colleagues here are French and your French is fluent and they don’t really expect that of Americans so maybe it’s alright not to arrest you. Now about those photos.
Erased! Look, all gone!
I took that trip seven years ago. Today I would be much more discreet. In fact, I’m not sure I’d have the courage to go just now. At least, if I went, I would see my friends & colleagues, give a class or two at the University, and come home with my luggage full of DNA from women with hereditary breast cancer risk. Skip the sightseeing entirely; this is no time to be a tourist there.
ABC Wednesday - with pictures, probably - is over here.

Monday, February 21, 2011

Sunday walk

I went for a new walk on Sunday. I won't say hike; it was just a stroll around the hill that's between my house and the really big hill where local hero Vercingetorix got the best of Ceasar and the Romans.
It's crisscrossed with trails and the odd bit of fencing that shows somebody's rights to this or that bit. Sheep droppings everywhere.
Happy to know I wouldn't be shot by hunters. Probably. I did spy plenty of spent casings scattered around.The view from the far side.
Spring seems to be coming to the far side of the hill, too. Surprising, since it's just a bit colder up a hundred meters.
There was plenty to see in the way of abandoned stuff. This shed seems to be useful still.
These tires and assorted groups of their bretheren were very slowly merging with the ground. I am fascinated by old junk and can fill my memory card with photos of it. An old mattress, boots, a car seat, junk you wonder what it was... but it got to be kind of depressing. Like this hill is more a diffuse junkyard than anything else. There were a dozen small vineyards gone to ruin (I'll go back for those in a month or two, to see what's still growing), patches of refuse, and ruts from the roaming motorbikes all over. Not much else.
At the beginning of the walk I reflected on what a neighbor said about digging in his yard. He's found several artifacts from the age of Vercingetorix (that would be 2000 years or so), and even the burial site of a chieftan - now housed in the Museum downtown. Wherever you turn it's history under the ground. That junk I'm seeing scattered around, in a thousand years will be archeological treasures!
Oh, here's another tree thinks it's spring.

I wish it were true!

Sunday, February 20, 2011

People I've known

The Poetry Bus is driven this week by 120socks, who set for us several possible destinations. I chose "I knew a person who..."
I knew a man who told me I should
told me I could
told me I'd better
I knew a woman who gave me paints
who read my story out to the class
who said Of course
I knew a man who never told me I could
never asked me what I wanted
who told me I'd darned well better
I knew a man who wanted to be my mirror
who asked how high and how far
who cast no light of his own
I knew a woman who tsk tsked
and shook her head
and wondered what I would come to
I knew a man who said yes and meant no
who said no and meant yes
and mistook me for his dark fantasy
I knew a man who does what he wants
and says what he thinks
and assumed I would go farther
All these people I have known
and have been.

Saturday, February 19, 2011

100 words: Pie

You won’t find proper pie here. Cakes, donuts, flaky pastries filled with cream, check.
I have to say, the Americans have something to teach the French in the kitchen, and one of them is


Not those prissy thin tarts they serve: deepdish pie.
They’ve got crust alright; what’s the problem with filling it up? Lest I not be fair - they do. With chicken and mushrooms and ham and potatos and that sort of thing stuck together with eggs.
No, I want it filled up with sweets, with spiced apples and sweet peaches and clever wild blueberries.
Real Pie!

Friday, February 18, 2011

Friday Photo Shoot Out: Twisted

Yes! I'm back at the Friday My Town Photo Shootout.
My participation is getting more and more sporadic. I could say this is due to being just so busy all the week and then wanting to relax intensely on the weekend so there's just no time for it.
But really, I'm just finding a new comfort level with the weekly themes I do. So I'll be back now and then.

You can hardly take a stroll around France without coming across patches of these twisted and gnarled plants. Auvergne is not known for its wine, but we still have vines mixed in with the pastures and the fields of corn.
Most of the vineyards within walking distance of the house belong to the Saint Verny cooperative, which makes a nice red. Surprisingly nice, according to people who 'know' wine. What I like about it particularly is the label.
French wine labels are largely stuck in the past, with a somber and predictable photo or drawing of the chateau attached to the vineyard, or just fancy text. Bor-ring!
The Saint Verny label has gone the more California route. In the States, you go to the wine aisle of the store and you're surrounded not only by delectable drinkables, but by clever and fabulous art gracing the bottles, calling for your attention. Colors! Shapes! Design! Done with the same old same old.

To join the My Town Shootout, click here.

Wednesday, February 16, 2011

Greatest film of all time: Dark Star

This from: http://mrlondonstreet.blogspot.com/2011/02/running-mates.html
I have a theory that every film enthusiast has at least one film they feel evangelical about which practically nobody has ever heard of. Off the top of my head I love Whit Stillman's Metropolitan and an obscure Australian romantic comedy called Love And Other Catastrophes. To finish off, would you like to pop on a soapbox and pitch about yours?


My film is Dark Star.
And, no, I don’t get to the movies very often. But when I do, I am enthusiastic, and I can become evangelical. Certainly with a film that was just perfect for the day I saw it.

Dark Star!
You must go see it!
Frabjulous special effex!
Stunning creativity!
Cleverer dialog than any other film, ever!

No, seriously, Dark Star was the feature-length graduate project of film school students John Carpenter and Dan O’Bannon. It inspired me for years afterwards with ideas for fantasy role playing campaigns.

Alright, what possible context could make this laughable movie a personal favorite? I was a junior in high school, going out to the San Diego Comic Con with my high school senior friends. (merely going out with people in the class ahead of you! it’s a big deal at the time)
This particular Con my steady boyfriend was out of town for the summer, and I went with another guy. Oh, yes! A guy who had already graduated. Who had a job, and a car. And indeed, this rather short series of outings did include the sweetest kiss at the front gate, rides in his barely roadworthy Volkswagon bug, feet up on the dash, Devo loud on the radio, and pizza evenings. And that of course resulted in his own steady girlfriend clawing him back to her (they are still married together).
So imagine then a certain teenage electricity in the air.
And imagine too a certain new sense of belonging in this group of afternoon gamers and fans of all science fiction, a place where the stranger you were the more you fit in.
And then looking at this film, and realizing that you could do that. The story is good but not beyond us. Undergraduate Philosophy for special dialog. The effects, well, pretty much anybody could do as well as that. Muffin tin space suits and ice cube tray computer consoles! I could be a filmmaker too, if that’s all it took.
So that's my film.
I haven't seen it in years.

Sunday, February 13, 2011

Poetry Bus with Icicles

It's Dana driving the Bus this week, and she has posed us a couple of picture prompts for this just-before V-day ride. I picked this one: They loved to go out and sit in the field
watching the sun down, listening to the blackbirds
sprawling, reading a book, talking some
the extended living room carefully too far from the phone.

The breeze of the open house caressed them
through the years the birds got to know them
and the grass grew up around the couch
They wore a smooth path
to make their way back in the dark
having greeted the stars.

It's been decades, and he is gone now
but she still makes her way
in the summer evenings
to their spot and their birds and their sunset.

Friday, February 11, 2011

100 words: Mainland

Yesterday's post was awfully technical, so here's a 100-word counterweight (am still working on "pie" - how to keep it to just 100).
If I were to go back to the mainland, my own that is, the motherland, I’d be stuck. I have yet again utterly forgotten to renew my driver’s license.
You need one there. No going without in favor of walking or the click and jiggle of the rails. But here I barely notice. A few minutes on the bus, a welcome and calming stroll, and the month is gone. The year is gone.
My friends think it must be such a terrible hardship, a constraint on my life. Not at all, here far from my mainland. I let it go.

Thursday, February 10, 2011

EMQN part 2

So not long ago I told you about how in our annual QC test my lab got an answer that was not the one posted by the agency. And now I have a response from them. It was indeed a trap.
At the end of that post I’m sure I lost you all in an explanation of how it could be a trap, but there’s a way to verify that and the original instructions explicitly said that this verification test had been done, and did not show the unlucky alternative mutation. So we didn’t repeat it.
But ahaaaa. Those original instructions I printed on Nov 8, the day we received the samples. An updated version of the instructions was posted on the QC website on the 16th, changing the key phrase to something ambiguous. The instructions are a 42-page PDF. Okay, only 15 of them are useful once you know how to use their website. But still. Am I going to notice the difference of part of one sentence on one page that says almost the same thing as before? I didn't.
Should I have?
Aw, geeze. Ideally, I should be perfect. This is a goal.
However they decide to score this year’s scheme, they did raise a valid point.
When you use quantitative techniques and find a deletion of a single exon, you should use a different test to back up the conclusion (in addition to repeating the first experiment on a new sample of course). This is because a small mutation could land right on the probe you’re using quantitatively, and prevent it from giving you the signal it should. That’s what happened here. Labs using the MLPA kit from a certain manufacturer should find a diminished signal for exon 11 of MLH1. Labs using other methods should find no difference at all and report the absence of large deletion/duplication mutation detectable by the method used (that there is indeed a point mutation in the sample is not their problem, because the method is not meant to detect them).
In practice, say I use MLPA and find a deletion of exon 11 in the patient. I test another sample from her, same thing. As long as I use the same test, and the makers of the kit don’t change that probe, any DNA with this mutation will give the same result. So I can follow the mutation in the family and give correct advice about digestive cancer risk. Of course it is better to have correctly identified the mutation. With the right mutation in hand I can use any appropriate method and detect it.
The big problem is when a relative in another city has their test done at their local genetics lab. I tell them what I found, and they go look for it using their own method. Their probe is in a different part of exon 11, and naturally it gives a normal result no matter if the person carries the mutation or not.
So for the QC program, the labs that used a different technique and saw nothing, they just say they found nothing within the limits of the test, and they get full marks.
Labs that used MLPA and report the definite deletion of exon 11 get the mutation wrong and get dinged for that.
Labs that used MLPA and report that the proposed deletion of exon 11 needs to be confirmed by a second technique get full marks. This was the point of their trick test. Only: the original instructions specified that a second technique had been done (and for that test to be normal and the MLPA to give a deletion means there is a deletion). Had they not said that, I would have worded my report to allow for this possibility.
The screw-up is in the wording of the original instructions. They said that sequencing gave a normal result, and this is not true. Sequencing is the very test you want to do to uncover this mutation. In fact, we went back and sequenced the case, and yep, there it is. Clear as day.
What I want to say is, these QC tests should be hard. They should give us unusual cases. They should try to trick us. But they can’t give us false information to work from.

Hey! No scrumming there!

From this week's Economist:
"Last year almost 360,000 (American) children played a non-contact form of the sport at school..."
no scrum? no ruck? no tackling?
Where's the rugby rugburn in that?
Oh, sure, a bit of lateral passing, some running up and down the field, a kick between the uprights now and then. That stuff has potential, I admit.
But ya gotta scrum! (touch-paauuse-engage!) ya gotta tackle! Throw the adversary to the ground. Get the ball! get it!

Wednesday, February 9, 2011

ABC Wednesday: D

D is for Darrell.
Darrell is on vacation.

Darrell has Dinner in his bathrobe.
Darrell the adventurer!
More ABC Wednesday here.

Monday, February 7, 2011

100 words: Facebook

JR: the man we loved to hate.
Fb: thing we hate to love. Useless timewaster, full of nonsense about what some cousin I barely know is thinking of having for dinner. Why do we share this inane minutia? Who cares?
Yet there it is, running in the background, behind spreadsheets and reports. My high school friend is taking the dog out? Trade you for the latest sparkling gem from my boss/student/tech. Love how the advertising on the sidebar changes to include a word I just posted. We think we are communicating. We’re just talking to ourselves and our big brothers.

Thursday, February 3, 2011

That time again

What is this?
What could it possibly be?
It's the secret access hatch in the front yard.
Every year I have to go out there, heave it aside, get down on my knees,
waaay down on my knees,
and flip open that blue lid to read the water meter.
And since the numbers on the meter aren't all that big, I have to practically get down in there to read it. Which you can see is a tight fit.

The special pleasure is this happens in the dead of winter, when things are either nice and frozen out there, or completely muddy. Or both.

Wednesday, February 2, 2011

A borrowed cat

And now for the Cat of the Month!
yes yes
I thought, my dear friends, there would be no cat of the month. Fresh out of fresh cats.
I've got old cats. But that would be reruns.
But wait, my friends Letitia and Bruno are coming for the film festival this weekend, and they have a cat.
Kikou is a miniscule Burmese.
I mean tiny! A six-pound wonder at most. But fierce. She'll claw you as soon as look at you, and don't be looking at her crosswise.

There she is! Beware.