Poetry to Improve the World

One of the several possible Poetry Bus challenges for Monday is to write about what we would do to improve the world. Jeanne Iris says so, right here.
Here's a first go. Perhaps a proper pome will come to me over the weekend; if that happens I'll post again!
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stop bitching
distribute chocolates
more cats
don't be infected by the bitchiness of other people's bitching, just fix the problem
pet the cats
no allergies
play with your toys
make sure everybody has toys
say "yes"
relax
breathe
have another chocolate
take time
listen
to the cats purring
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2010

Last workday of the year and we’re down to four people. After noon, maybe three, maybe two. Perhaps I won’t be there to count.
It’s been a calm week at the lab. I like this time of year, when the year-end rush is over (or given up on!), everyone’s on vacation, finally a bit of peace between the two party weekends. It might be nice to travel and see my family for the holidays, but that always turns out to be so hectic and bothersome. Stations and airports are crammed, and may close for bad weather for any length of time, plus since so many people are traveling it’s more expensive, more hassle, and there’s never anyplace to sit down. Forget it! Travel in the off-season.
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So what sort of year has it been?
Every year, it always seems to have the busiest year ever. Which in a way is true, since the annual activity report shows that, yes, we did churn out more reports than ever before. (This doesn’t have to mean we did more work, just that we were more successful at it. No matter how many times you repeat an assay, only the one that worked becomes a result.)
By a lot of measures, I was busier, but not by one of the measures that my boss has really been leaning on me about: publishing. The lab has three new permanent employees, which makes the lab as a whole busier, which makes me busier because I’m the one to manage all those people. The lab must attain accreditation in the near-ish future, which may seem far away, but we are so far away from being accreditable that it’s urgent to act now. I can’t delegate much of that work until I come up with the framework for how to do it.

Translation: It was the year I reached my managerial capacity.
That’s why it feels like the heaviest year ever.
There have been worse years. The one I spent as a post-doc at Yale was pretty awful. The second year of grad school was horrid.
But this year I feel I’ve really done all I could to make things run, and it’s just quantitatively too much. I’m tired. Thank goodness this week is just coasting, or I would collapse.
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On the other hand, this was also the year I got off my duff and joined some new social circles. Italian on Thursdays, which I fully intend to go test in Italy. Bridge on Wednesdays and assorted Saturdays, where I’ve become an appreciated partner. I’m learning people’s names, becoming comfortable playing a session without too many mistakes. Last night I acquired a regular partner, even, so I won’t always be arriving to play and have to wait to see who else might show up on their own. It’s neat to become part of the group, not just a visitor.
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Travel happened. Of course!
There was San Sebastian, on the spur of the moment. Wonderful place. Must eat my way across Spain some day. Poitiers for one of those long weekend explorations I really must do more often. Strasbourg for a conference, in the January snow.
And a magnificent road trip to see my family and some friends in the States. We had everyone together for once, as only happens every few years. I even picked up my last Southern state: Alabama. Just three to go!
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And New Year’s Eve? well, I think I’ll just relax at home. If the weather’s good, a day hike or an overnight train somewhere might be in order. I’ll work on Monday’s Poetry Bus ticket, finish up the Best of 2010 photo album, and take plenty of naps in preparation for the full-speed-ahead first Monday of the year.

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Oh, a talk, erm...

So I’m writing this paper on a project that my boss imposed on the laboratory. As you might know, because I’m a complaining sort of blogger at times, and I’ve wailed about this thing before. The idea was to go fishing for mutations with our fancy new sequencer in a kind of tumor whose origins remain mysterious. We couldn’t cover the whole ocean of possibilities, so we stocked the pond with a reasonable list of candidates, and indeed hauled out a bunch of mutations. Six genes times five tumor characteristics isn’t that much analysis to do.

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Over the summer, I sent around a draft of the paper, and it came back that it might be very useful to complement the mutation information with info on the expression of some pretty common markers that interact with the genes we found mutated. That would tell a more complete story, and the work wouldn’t take long. Just five protein markers.
Five isn’t too many.

But every time you add a marker, you need to compare it to the results of each one of the others. The amount of number crunching to do goes up exponentially, and the different possible combinations of results far exceeds the number of tumors we had to look at.

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Fine. I did all that analyzing and hoped to find the new data neatly confirming what we were learning from the mutations and consolidating the tumors into a small number of groups with similar biology. Getting a handle on the biology might give us new therapeutic options.
Only, no, that didn’t happen. For every two the same, one was different, any way you looked at it.

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It was like thinking that (kilt + bagpipe) might = Scots, and then assessing haggis just to be sure.
Well: kilt could be Scot or Halloween, bagpipe could be Scot or Breton, and haggis could be Scot or just weird. And none of the bona fide Scots are required to have kilt or bagpipe or haggis at all!
Things just fall into chaos when you don’t have enough samples for the p values to get really small.
**Sigh**

So the new paper has been written and sent around with a plea for advice (and not just my awful English, please!), and after a month only one of my faithful coauthors has responded. She, alas, seems to have dug up the old version to advise me on.

Meanwhile, the guy whose idea this all was in the first place remains silent. Oh, except to schedule me for a public talk on this very project a mere three weeks from now.

Thanks. I’m honored.

weekend walk

I had a cold over Christmas, and on the 25th didn't budge from the house. Never quit my bathrobe - just went from nap to book to dvd. With a few trips to the kitchen.

Sunday was better. We had half an inch of snow in the yard on Saturday, and I hoped there was rather more up on the nearby hills. It was a bright day and very cold, but I bundled up with extra socks, and tights under my jeans, and many layers under my parka. Hat, mittens, extra handkerchiefs, the whole nine yards. Last year I picked up some of those glove-mitten things, where the mitten over the fingertips is a big flap you can pin back, revealing gloves that don't cover the last finger joint. Perfect for maneuvering a camera without taking off the handwarmers. They made a new trailhead that leads up the Gergovia plateau, and it passes through this huge yard full of odd metal sculpture.

Plenty of mistletoe overhead.

Icicles on the windmill.

Critters had been all over this road. Half a mile down, I discovered why none of the many human traces went that way - it was a dead end at one of the groundwater monitoring sites.

Not much snow on the surrounding hills at all.

Cows have been moved into their barns.

Have a good week!

Rule: do not regift to the original owner.

This week’s poetry bus is being driven by Muse Swings, who set us the task of writing about our worst/most useless/most disturbing/most painful/stupidest/ugliest/least appreciated/most disastrous Christmas present. A nice antidote to all this good cheer going on.
I’m not sure a poem is forthcoming, but I will tell you about my most disappointing gift.

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I was 8 or 10, and the apple of my grandfather’s eye. When he came to the house and deposited the presents for my brothers and me under the tree, he held mine out with a mischievous smile and said he just knew I was really going to love it.
Oh my, I thought, I’m going to love it! What could it possibly be? The package was long and thin, with something lumpy inside that rattled when you turned it upside-down. I spent a whole week wondering what could it be, with such an odd shape, going back again and again to shake, squeeze and fondle.
Finally, Christmas came.
Usually, we’d go straight for the gifts from “Santa”, because they were always the most fun. Santa always gave toys, never a pullover. This time I went straight for my mysterious gift from Granddad, tore it open at last, and what dropped into my lap but an old string of beads of mine I’d forgotten at his house over the summer.
Oh!
Oh, those.
Hey, that’s no present at all. It was as if my grandfather had given me nothing. I hope I kept from crying, but I don’t think I did. I know he really did think I’d be thrilled.

So, belatedly, Thank you!

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Slumdog Irony

On this eve of Christmas eve, I'm home with the cats, sick with a headcold and pampering myself such as I can,

...smoked salmon and toast, a nice Reisling, hundreds of white christmas lights strung around the room, chocolates...

and I'm about to watch Slumdog Millionaire.

For the first time.

Yes, yes, I've never seen it. I miss a lot of films because I don't want to see the dubbed version first, and the original only stays in the theater for a week (if at all). But there was this great sale on DVDs over the summer, and I've got several left to watch for the first time.

This particular movie, with all the noise about it afterwards - how the child actors in it were paid a pittance and went right back to the slums so poignantly portrayed - I just wonder how experiencing the bouhaha before the movie might change my viewing.

...

...

Wow.

I must say, that is one great film.

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The fairy tale ending, however, is a little too good to be true. It's as if the polemic around the moviemakers making a killing but the cast not rising out of their poverty is a continuation of the film, a next chapter in which you see, no, the fairy tale doesn't last. It's an epilogue that tones down the sticky sweetness of the end, coming back to reality.

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Weaver's Star Poetry Bus

Wait for me! Wait for me!
Sorry I'm late this week for the bus. The Weaver of Grass suggested Star, take it as you will. So here we are:

Star
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It was shining in the north
didn't look so far away
looked as if you could touch it
if your finger were just a bit longer.
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Let's go there, she said,
We'll see it up close
See what it really is.
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So they went
across the fields and beyond the river, up the mountainside
They went through villages and cities and saw things they'd never seen before
They went through place where the language was strange
and the food indescribable
They saw new friends and old relatives,
were waylaid, made progress
they went on and on, as the seasons turned around them
forever on, crossing oceans, growing old.
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They journeyed until they were as close as they could get
Jump!
Leap high and catch it!
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But it was just as far away
as always.
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Catch the bus here!

IPYPIASM in action

Yes, yes, I did go out this morning and slip some poems (alright. I admit it's just copies of one poem. But I figure that no particular person is going to find more than one of them, so it doesn't matter they're all the same.) Poem in a pocket.
Poem pretending to be shoes.

Poem among our Fabulous National Champion Rugby Team's books.

Poem in the chocolate Santas.

And finally one in the coffee maker aisle, a hurried shot as the salesperson came up, wanting to know why I was taking pictures of the merchandise. Thought I was a spy from a rival store!

Uh, no, just checking this is the right brand...

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What it says is here.

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Holiday cards

I love getting holiday cards. Finally some mail that’s cheerful and fun and personal!

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I received a card yesterday from a close relative, one of those studio photo montages of the family in their finery. Flipped it over to read the message, and it was just blank.
Oh.
I’ve been checked off a list.
I was really irritated. From cousins I’ve seen twice in my life one might expect a simple signature. But after having sent a package of cottony/wooly items of my own design and execution, plus some chocolates (they will like the chocolates, at least) off to them just last week, it’s kind of a splash of icewater to get this card. I was hoping for a letter, some news, something personal that confirms yes, we are family.
Then I remind myself that it’s not a race, no scorecard. So what if I sent them something? That’s up to me. There’s no quid pro quo going on.

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What do holiday cards mean to me, anyway? That might have nothing to do with what they mean to my relatives.
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In the chilly evenings of the end of the year, I like to take the time and catch up, or at least connect, with my friends and family, and writing holiday cards is a large part of that. I love to write, and all year long I tell myself I should find time to write to people (not just to the mostly invisible audience of the blog), and all year long I don’t get around to it. Card season is the warning light that I’ve really got to get down to it. Sitting in a corner of a busy pub, with a glass and a fountain pen and a stack of cards is a great way of passing an hour, repeat as necessary.

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Some years I write reams. I include extra pages in with the card, which is crammed with writing top to bottom and maybe some on the back.

(yes, this really did happen)

(yes, I know it’s been a while)

(No, I won’t put it in the past tense and admit it will not happen again).

Then I got busier, or tired-er, and didn’t put anything more than would fit on the left side of the card. Now I’m down to writing some heartfelt but not terribly original greetings and wishes, in script that is a bit larger than necessary, and I’ll be happy to write to everyone if even just a little bit.
What I like about sending cards is taking the time and sending a personal message. If there’s a pre-printed message, I add one of my own, but usually the whole message is mine. This is me. I’m wishing you well.

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What I like about sending cards is imagining my card being placed on a mantle among the others, so colorful and diverse, in a soul-warming bouquet of happiness and good thoughts.
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There is, of course, a second motive to all this sending.
Receiving!

Send me cards! Fill my mantle (actually, I string a ribbon along the wall or across the room, and hang them on it). Say hello. Say you love me and hope I have a wonderful new year.

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Friday Photo Shoot Out: Red

I'm not very well prepared for this week's shootout, but with red being my favorite color, I can hardly miss it when taking pictures in the house. These are all from the archives. Red rug in the bedroom.

Red cover on the armchair.

And a red throw on the couch.
More Shootouts here!
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IPYPIASM

That's International Put Your Poem In A Shop Month, for you reasonable people who do not concern themselves with leaving small pieces of paper in mercantile establishments. The rest of us, we know what it means.

Thing is, all the shops around here are full of french people. They’re expecting french poems. For a while I was thinking to write my missives in English, as I usually do, but it's possible that the surprise of coming upon a random poem like that is startling enough and if it were in English people would just crumple it up and toss it aside. So I've come up with this:
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Le soleil
Il vient tard, il part tôt
Occupé avec ses soucis australs
Si nous, on fait un gros, gros fête
Plein de champagne, plein de cadeaux
Revient-il nous voir ?

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and will be printing a bunch this evening for placement on Saturday.

Wish me luck!

Ah, yes, that's:

The sun

comes late, leaves early

occupied with his southern concerns.

If we have a great big party

with lots of champagne, lots of presents

Would he come back to see us?

this & that

The jam collection. It was a tough pick which one we can do without, but finally it was decided:
This one is off to South Carolina. The jam; not the wind-ups. They're off to Scotland.

And the cat tree, strategically placed in front of the radiator, is at last fully occupied. In about the right order!
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The penultimate Cat of the Month: Sienne.

Sienne is small and skinny. Maybe it’s just the marks on her face, but she looks scowly all the time. And she’s got this whiny complaining meow. Just how some cats are.
The other cats are classic feline layabouts whenever they’re inside, but Sienne likes to play. And play, and play. There’s a whole collection of things under the kitchen cupboard/table that I’m not really looking forward to finding again when I move some day. Anything at all that ends up on the floor there is great fun at night, until it ends up out of reach.
Then there’s the Shoelace. Hours of fun can be had chasing the Shoelace as it is dragged along the floor and over the armchair (where Bandersnatch is trying to sit with some dignity).
Sienne is afraid of people, except for my brother. For four years now I’ve had the same guy come feed the beasts while I’m away, and he has never once even caught a glimpse of her.
Sienne does not go out. Well, she will go out if I’m out in the yard. But she doesn’t go out when I leave for work, or overnight, like the others do. She’s a homebody cat. She likes to be on things. On the towels, on the desk, on the tall armoire, on whatever there is to be on.

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The presents!!

Has it been a week already?
What? More than a week?
I'd better get on the ball, then, if I'm going to get (two of) these out in Saturday's mail. I have just printed out the list of our seven participants. Cut it up. Folded up the bits. Picked three.

The winners of the Fabulous Present Giveaway are.....
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Mark!
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... and...
Titus!
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...and...
steven!
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I was thinking of assigning the gifts randomly, but we all know how Titus feels about small windup toys. And then there's a warm scarf in dark green wool & alpaca that's shaping up very nicely, but Mark lives in the land of No Wooly Scarves Necessary, so that may be better with our friend steven of the Frozen North. Send me your snail mail addresses by email, and happiness is on it's way!
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for T

well, yes, it's sideways (I can set the camera down on it's side, but not upright. Little design fault there. And Blogger won't let you turn a video sideways.) And the lighting is all red. But I know you want to see more, Titus!

ABC Wednesday: U

For this ABC Wednesday, I bring you this special documentary film featuring the prototype robot UB445.

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get it while it's cold

Just a few shots in the back yard from last week's snow. We didn't get quite enough to shut the town down for a day off, or even properly cover the yard. I was lucky there was some left Saturday. It's gone now.
Where the melt drips off the eaves.
Queen Anne's lace nice & frosty.

And a very late apple.

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Pubpoem

This week's Poetry Bus is driven here by Kat, and our task is to take the name of our favorite pub, turn that into characters, and write a fun poem with these characters. Well, my favored place for a beer and a big-screen rugby match happens to be called the Garden Ice. Who knows why. Neither "garden" nor "ice" is french, and when you put them together it still doesn't say anything.

I leapt up in the morning
happy for Saturday
bright sun through the window
cats fervently wanting out
Let's go out and pick fall leaves from the lawn
and taste the last apples from the trees.
I open the door
and the cats come barreling back in
It's cold out, Mom!
the garden is covered in ice!
December has come.
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Presents!

Today at Have Genes will Travel, we're getting into the end-of-year spirit. It's a spur-of-the-moment thing, and it may take me until the weekend to get pictures up, but here we are: NanU's Fabulous Present Giveaway. Just leave me a comment saying you're in, and I'll hold a drawing for the following gifts (worldwide postage included):

1. A jar of home-made jam. There's apricot-thyme, apricot-ginger, apricot-lavender, blueberry, cherry, and blackberry left in the cupboard, so specify a preferred flavor if you have one.

2. A scarf that is yet to be knitted (don't worry about that - scarves go quickly!). Cotton, wool, alpaca, and rayon available.

3. A pair of wind-up dinosaurs, about 2 inches tall.
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Not even this week's bus

The Poetry Bus comes around too often these days. Already this week’s ride is disappearing around the bend and I’ve had all of about five minutes to consider my poem.
Sometimes that’s enough.
But sometimes there’s the sort of prompt that really deserves a bit of thought, and care, before being allowed out in public. The latest one is one of these: argue with god. I’m not in the mood for some flip little thing, four lines and a sting. The eventual poem may well be four lines long, but they’ll be well-considered ones. A few weeks ago we had The path not taken, another topic that deserves far better treatment than I’ve been able to give it.
Where to start?
Which one to pick?
There have been some radical options. One of the big ones happened in 2002, the September I got my current job. The other road there would have been ... um... I have no idea what it would have been like.
I was coming to the end of the possibilities for temporary contracts at the Center. I had been a post-doc for two years: that’s done. Then an Assistant at the University for a year. Then I was paid through a charitable organization for a while. And that’s about as far as a foreigner could go without winning some kind of permanent contract. Grant after grant was turning down funding my salary.
But I didn’t have anything else lined up. Job searching takes a huge amount of effort, and I had preferred to invest myself in the work I was doing, in hopes of a good publication that would make funding easy. So the end of my contract loomed, and there was no After.
Thinking about After was so stressful I just didn’t.
What would I do? Where would I live? If I moved back to the States, a ticket I could barely afford, what State should I go to? I didn’t have a job in any of them. What would I do with my cat?
Finally, I figured I would sell all my stuff (how? To whom?), give the cat to a friend, and just become one of those after-college people, traveling around and taking pictures and writing about it. I would become a travel writer. I would have adventures and recount them with wit and sell these stories to magazines and newspapers and whoever buys those sorts of stories.
Never mind I had no clue how to go about shopping my writing around. Never mind the little I did know said the creative writing biz was nearly impossible to just break into and make a living at right away. And travel photography! Hah! Looking at my bank account, two unsalaried months of rent would be it before going red.
That was the plan.
I was fresh from reading a memoire of a guy who joined the Peace Corps and spent a year in Africa, showing people how to farm fish to improve their diet and make some cash. Incredible story! Not only did he get to have this fabulous year, which was often difficult and discouraging, but always intense, but he published a book out of it. Perhaps the PC would take me too.
So that was the path.As you know, I didn’t take it. My boss was casting around for a person to run the diagnostic lab, and I had thought he didn’t want me for the post, and he had thought I didn’t want the job, but we eventually cleared all that up and here I am.

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I'll always wonder if I would have survived out there, my home on my back, hoping for something around the bend.

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On the tail incident.

About two weeks ago on my other blog I posted a story in which the stuffed rat Bjorn had his tail damaged in a disagreement with the other rats.
Why this tale of violence?
A couple of things:
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It was really a story of sibling or schoolyard rivalry, and how kids can gang up against one who seems to be too favored by the adults. In their attempt to put the other in his place, they go too far and try to cut his tail off. (Which doesn’t work entirely, but that was a technical problem - I was hoping the pruning shears would do it.)
None of the rats admits or complains to Maurice that there was any problem at all. No ratting, no whining.
It’s like the time when one of my brothers was picking on the other, who then broke one of the large windows at the front of the house. Rather than point the finger and get the other in trouble, the first brother hightailed it to the shop to buy an new windowglass and install it before our parents got home from work. I’m not sure they noticed the window right away, but the hole in the front door was still evidence of an altercation.
But anyway, when you’re little you might go running to Mom or Dad but when you’re a bit older you keep the kid feuds between kids.
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The other thing, it was just plain fun to go over the edge. People don’t expect that.
Toys don’t usually get better after you break them. But why not do it? Now I’m big, and employed and all, I can buy as many Ikea rats as I want. They’ve got them by the bin-full! Why not a tail off here, an explosion there, a bit of disembowelling, why not? There’s an exciting devlishness in going through with the threat. Now you’ll never know if next time the toy will make it to the end of the post. How about my wind-up dinosaurs, Harold and Marguerite - fun little guys, hmm? How would Harold do against a 16-ton weight? Wile E Coyote always got up afterward and staggered away...
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So now Bjorn has a band-aid holding his half-severed tail together. I may have shocked a few readers into not coming back, but I can live with that. I don’t like it when all the endings are happy - you stop allowing for the possibility of not having a happy ending, and the only suspense in how long it takes before the deus ex machina comes.
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Not even December

So I was hoping to turn over some more of the vegetable patch this weekend, and get it mulched for the winter. But when I opened the door there was this.

Natalie's been out.

And the veg patch looks like this. Sad old tomatos. Looks like having done half the area will have to be enough!

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Friday Photo Shoot Out: Favorite Shop

I would have been with the crowd showing chocolates & pastries for the Temptation theme, but I figured I would leave that for this week. This isn't my real favorite chocolate shop, but they had a huge truck parked out front and I just couldn't get a photo!
So many choices!

And of course the ASM.
No, their shop isn't the greatest (too expensive, and the team socks have too much polyester), but the team is.
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For more Shootouts, click here.

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Existing

I never did finish my P-bus poem for today. So typical of my days for weeks now, maybe I should just take some things off my calender altogether. But no, not the fun things! Here's the fragment, which on its own has a certain enigmatic quality - you'd never know the theme is to write about our lives. Perhaps I'll finish the thought for another week.
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Like a rock in a stream
Water going by
Just going on by
Taking bits with it, tiny microscopic bits.
In time, worn smooth
A long time
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Click here for other takes on Enchanted Oak's theme.
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Trials and tribulations of a manuscript

First review:
Who cares? A piddling paper on a piddling family. The authors have this one unusual family, and from there are suggesting the whole world change the way people with mutations in this particular gene are treated. One family is an anecdote. Just because they escaped getting stomach cancer* doesn’t mean that the next family that comes around shouldn’t be recommended to have prophylactic gastrectomy. Get outta here!

Alright, that’s a pretty crude paraphrase, but you get the idea. Our paper was very forcefully struck down. While naturally depressed at the failure, I was secretly satisfied that the complaints were exactly the points I thought my coauthors insisted too heavily on. But such are the squabbles between coauthors. I have something of a reputation with my boss for setting my sights too low in submitting papers. I don’t set them too low: I really try to send a manuscript where it has a decent chance of getting in.

Admittedly, if you don’t shoot for the stars, you’ll never bag one. But I hate the multiple rounds of rejection this entails, plus the precious time lost at it. If my performance review says my goal is to publish 3 papers this year, should I really mess around with fanciful submissions that will never succeed? And I play a certain counterweight role against my boss, who is thinking Nature or Science every time we have the least result.
So we (I) revised, and added a second, smaller family with the same story that we’d found in the meantime, and submitted to a very good, though not quite so lofty journal.

Second review:
Nice paper, but not big enough news for us. Get a dozen such families and we'll consider it.

Finally the senior author was convinced that the top journals weren’t interested in our story. They have bigger fish to fry. So we resubmitted to a good, middle-level journal.

Third review:
Nice paper, very important for the medical community. Will be one of the milestone papers in the changing evaluation of the effects of mutations in this gene. A few minor modifications, and we’ll be happy to publish it.

Certainly, this wasn’t exactly the same manuscript as the first submission; we rewrote in view of the first batch of criticism. But it’s essentially the same message, based on the same family. And it's the level of journal I wanted to target in the first place. I'm just very pleased to get to the end of the story!

*this is usually fatal, and terribly hard to catch early. Prophylactic gastrectomy (removing the stomach from healthy people at risk) in young adults is the only reliable way to avoid it. But just imagine living the rest of your life with the dietary restrictions that involves!

Friday Photo Shoot Out: Temptation

These days I'm very tempted to stay in bed in the morning.

No matter how much laundry & how many cats pile up there.
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The Shootout is here.
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I’ve finally joined the Italian club.

Yes! It’s been a month already, in fact. Two.
I’ve had three lessons, but yesterday was skipped for the holiday and the week before was skipped because our teacher was recovering from a minor medical thing. So it’s been:

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Lesson 1 with a woman who doesn’t usually teach beginners so she didn’t know how the book worked and wasn’t ready to get us started learning a whole different language. (I really admire people who teach entry-level classes in a foreign language. I may know how to speak/read/write English, but I’ve really no idea how I’d go about teaching that to someone who didn’t at all.)
Lesson 2 I had to skip for a meeting out of town.
Lesson 3 I prepared for by reading up and doing all the exercises for “Lesson 2” in the book, thinking that would meerly catch me up to where the others were the week before. But in fact, that evening’s class covered just about the first third of “Lesson 2”. Aha. The book’s lessons correspond to what a college student might do in a 2-hour class. But this is a more or less casual club, a hobby sort of thing. The students are all middle-aged (I’m the youngest! I love being youngest once in a while.), and nobody wants the kind of cadence the book offers. So we’re getting through it as we get through it.

Lesson 4 covered more of “Lesson 2”, but didn’t quite finish it. We’re all still at the frustrated stage where we don’t have enough words yet to say anything.
And now this 2-week break before getting back to it. I don’t know what people will retain from the early lessons by the time we meet again. Might have to start over!
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I think learning a new language is mostly a vocabulary thing. Plus some lessons to show you how to put the words in order, maybe a bit of conjugation. Of course. Essential. But if you have some vocabulary, you can start using it to express thoughts, even if the results are all garbled up in your own usual grammar. We all know the mistakes that non-English speakers make when they talk to us. But switching the verb and noun around isn’t such a huge burden to understanding. Yes, well, there are plenty of examples of how getting it wrong can go very wrong. But overall, you can get something across. And if you listen to films in the language, and read books or magazines in it, or go there and talk to people, you find out pretty quick what the major rules are.
Italian isn’t so different from French. Both romance languages and all that. Half our words in English are pretty much the same ones in French or Italian or Spanish. (The ones that aren’t can be counted on to be German or Greek.) When I came to France, I found that English with a cartoon-french accent worked pretty well. Should be the same with Italian! Right?

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So I bought a book in Italian last weekend. A slim volume by Primo Levi, a book I’d read before in translation. Perhaps I could have found something happier, but the selection barely covered one narrow shelf and at least with this one I have an idea of what’s going on.
Thus far I’ve read about five pages. There’s a balance to strike between making a dictionary pause for every word you really can’t imagine what it might be, and barreling through with these holes in your understanding because otherwise by the time you get to the end of the sentence you don’t remember how it started.
But I’m doing it. I’m reading in Italian.

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Friday Photo Shoot Out: Overhead

Look up these days, and what do I see.

Miss Fluffy on the fence.

"Sun-dried" apricots.

A few apples still.

The occassional flying rabbit.

Accompanied by some jumping rats.
The autofocus doesn't like this sort of moving target!

Oops. Get the ladder out.

Birds in trees are more visible these days.

But mostly the things hanging over my head are on my desk.
Or maybe it's me sinking under them.

I am definitely in over my head these days.
Like this paper.
I hope it will be leaving for a journal in the next few days, along with two others.

Then life will be better.

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Join the Shootout here.
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some science for ya

A quick word about how this sequencing thing works, then. A strand of DNA is made up of four different nucleotides, A, C, T, and G. They're mixed together pretty evenly, with a slight excess of A's and T's. When there's a stretch of one nucleotide repeated, say 8 A's in a row, that can cause problems when you want to replicate the strand. The polymerase (the enzyme that makes new DNA) can lose count, and do only 7 before going on to whatever comes next. Isolated polymerases in the laboratory make lots of that kind of mistake, and although the replication machinery in our cells (which includes the polymerase but also dozens of other proteins in an enormous complex that proofreads and makes sure the replication is faithful to the old strand to be copied) is quite good at making good copies, these 'homopolymer' sequences are often the source of mutations. A mistake is made, a base lost, and everything that comes after is out of phase.

So when I'm looking for mutations in a gene to tell a family where their cancer risk comes from, I pay special attention to these homopolymers.

Our new sequencer reads sequence by a trick that means each base incorporated into the strand being synthesized emits a certain amount of light. One base, one unit of light. Two bases of the same kind, two light units. The counting is pretty good through 5 bases, but once you get up to 7 or 8, it's hard to tell exactly how many units you have. Ten identical bases in a row, and the machine doesn't have time to get through all that in a single cycle, and so you just can't read 10 or more.

Our sequencer also reads each molecule of DNA that you give it one molecule at a time. Each one is called a 'read'. The software lines up the reads against the reference sequence and tells you how many of what kind of bases you have from start to finish.

Let me show you its counting problem.
The software knows that you have to have a whole number of bases. 7 or 8. No such thing as 7.6 bases. So it takes all of the reads with intermediate values for the number of bases in a series, and rounds off to the nearest whole base.

With data like this, no problem. The dark bars is what the furnished software says, and the light bars come from our own analysis of the raw data, admitting fractions of bases. 87% of the data rounds off to 8 bases, and that's great.
But most of the samples come out like this. The furnished software says about 45% of the sample has 7 bases, and another 39% has 8. If all I know is these two numbers, I'm thinking there's a deletion of a base on one of my patient's two copies of this gene. But look, there's clearly (well, okay) a single population of values, centered at 7.4 bases. This sample does not have a mutation, it has a bunch of intermediate data that's been incorrectly interpreted. I analyzed this one using a different method, and there is definitely no mutation.

So what about this?
This is just exactly what I expect from a real sample with a deletion of one base on one of her two copies of the gene. Ironically, the commercial software gives me exactly the same values as the preceding example! The second experiment to confirm or reject the proposed mutation is underway, but it looks pretty good. Two populations of values. The difference between the peaks is not exactly one base (it's 0.8), but it's pretty close. If this sample doesn't have a mutation, we'll be having some serious talks about the technique. I have some other examples of real deletion mutations, and they look just like this.
What really kills me is this sample - and these four graphs come from four samples in the very same experiment, showing the same bit of sequence. This data is ugly. I appear to have two distinct populations, at 7.2 and 8.1 bases. But the trough between the two is not so clear. And it's not so symmetrical. I do have the confirmation experiment done for this one, and guess what:
No mutation.
All the DNA has 8 bases.

Not 7. Not 6.

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sigh.

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No, we did not miss that boat.

Boss just back from the American Genetics meeting, all in a huff we'd been scooped.
Ah, boss, it's true we didn't submit an abstract to this meeting (we didn't have any chance of actually going, and didn't know you planned to), but look! The authors are our Belgian colleagues! We're on that paper. The program they mention for treating homopolymer data is ours.
And yes, the manuscript is millimeters away from resubmission.
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Poetry Bus goes bathing

Jessica set the bus destination this week: bathing. Click here to sign on and take the tour.
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The pleasure of the Bath
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Nothing better
than a candlelit soak
while it snows out.

Damn this drafty old house
with its shower stall.
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Magpie 39

Oh, look, a pile of leaves. I wonder if there's any bugs.

bugs ;;; bugs ;;; bugs

Oh yes, bugs. Very juicy.

buUUgs!

There's Clara. She wants my bugs.

I'll peck her if she tries.

peck.......peck.......peck

thinks she's so fine in her red feathers

I'll peck her. She's not getting mine.

buUUgs!

Oh, there's Rocky. Sooo handsome

Shake my feathers out, yes. Ohhh yes

Bug! got it.

Rocky's scratching in the dirt, looking us over with his bright eye,

Here! Right here!

I'll just walk over to that tree, show him my good side.

Here's Bess, strutting around, thinks she's so fine.

Get out of my way!

Peck you! I will.

Doesn't know a grub from a piece of wood, that Bess.

Ain't no bugs over here

bugs ;;; bugs ;;; bugs

buUUgs!

Oh, here's the Farmer! Where's the bucket of corn?

Where is it!

Gotta get there first Gotta get the corn.

Where is it? Get out of the way, you chickens!

Peck you! I will!

Here's a nice pebble. I like that one.

Here's the Farmer. He's picking me up!

He's got my feet! Help!

He's taking me away!

buUUgs!

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For other Magpie 39 Tales, click here!

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