Thursday, December 31, 2009

Friday Photo Shoot Out: Under Construction

This week's Shoot Out theme is Under Construction. Ho Ho. I just happen to have a construction zone right outside my window. The Centre Jean Perrin is modernizing. Has to: the health department would shut us down otherwise. Here's the plan. That helpful arrow shows where my office is right now. Yeah, in what will be a parking lot. For the moment I'm still here.
A couple of months ago they started digging on our side of the hospital.
The backhoes came right up to the wall - our secretaries' office is just on the other side of that wall and sometimes they thought the machines would break through.

Then the foundation was laid and a forest of reinforcing rods sprang up, like grass after a rain. It didn't take long for all those rods to be encased in concrete walls.
Now we look outside and see the embryonic windows of the new radiotherapy department.

The construction makes our little annex tremble so much that our cat sometimes hides in the copy & mail corner.

Out front they have a much bigger hole to dig.

This is where the new hospitalization wing will be. Only 86 beds or so; it's smaller than our current capacity, and they'll all be private rooms. It seems strange to go to the trouble to make a whole new building, a larger one, and put in fewer rooms, but they say they're moving toward shorter stays and more outpatient care. With the higher turnover, we're expected to care for more patients, not fewer. I'm not convinced of the math.

So they're working on it.
I'll keep bringing the camera once a month or so, keeping track of the progress.
What a lot of us really want is a multi-level parking lot, but we're not likely to get one. Every time they build here we lose parking, and none of it is ever replaced (the parking area in the model does not quite make up for the lost spaces they've dug up already).
Happy New Year, everyone!
To see the other Shooters, click here.

Wednesday, December 30, 2009

Not-quite Thursday Zebra

Yes, it is a fact of life that zebras on the wild plains of Africa have much to fear from the big cats that roam the area, looking for a good meal for the husband and kitties.

Today's modern housecat might bask in the warmth of the radiator when the sun is far away, but their domination of housezebras remains.


Monday, December 28, 2009

His Wife

I think I've just figured it out.
Of course, I could have answered the question meerly by going into the visitor's center, but at the time it only seemed like a minor curiosity. Then it turned into an annoyance, and led to a certain amount of indignation, but by then I was far away from the visitor's center, in a different country even. So I continued to stew, until I found one of those 'well of course' answers.
In the National Cemetery featured in my last post, members of the military have their name, grade, dates and sometimes posts engraved on the headstone.
Then there are whole sections where the headstones have dates, but no names. This is not a place for the fallen whose remains could not be identified with certainty. They're marked "His Wife" or "His Daughter". I suppose there must be "Her Husband" as well, though I didn't see one.
It's not possible to know who's wife or daughter. There's no name on the stone at all, either his or hers. There's no grave nearby that the nameless woman is associated with. If you go there looking for your Aunt Mathilda, you just have to know where she is.
I thought it was awful, to be stripped of all identity like that. "His Wife". Not only does the woman not deserve a name, but not even her husband's name is there. Mrs Jones taken an appalling step too far. These names were not lost, they were deliberately deleted. Reduced in death to an appendage of an anonymous "Him".
But then it is a military cemetery. Women from the services have fully informed headstones. Spouses and offspring who were not members of the military, however, don't receive the same level of recognition as those who were. It makes perfect sense from that perspective. You might debate whether spouses and children have their place in the National Cemetery at all, and I guess this is the compromise. There are no family groupings, no names for non-servicepeople, but they're there within the gates.

Thursday, December 24, 2009

Friday Photo Shoot Out: Angels

This week's Shoot Out theme is Angels.
I don't have any of my Normandy photos digitized, but this is Fort Rosecrans National Cemetery in San Diego, where many American angels rest overlooking the sea.
Thank you!
Angels posts from other Shootout members can be found here: be sure to stop by!
Merry Christmas, all!

Wednesday, December 23, 2009

Poetry Go-kart

The fabulous Mr. Eejit has fixed up a new vehicle for us:
Santa's Poetry Go-Kart Ride!
This is a preliminary effort while I get myself into the holiday spirit.

Emptied out

Everybody has gone.
They are gone into the shops to acquire that one last present
They are gone into the hills to slide on the snow
They are gone to their families on the other side of the rivers and the plains and the mountains
They are gone to their homes
Cozy in front of the fires and the twinkling lights

They are gone, their arms laden with gifts
Their trunks full of luggage and groceries
Their dogs on leashes yapping and jumping with excitement

They are gone from the lab, which is hollow and dark

And in an hour it will be my turn too.

Happy Holidays! Go on! Get outta here! Get out and celebrate!

Thank you Eejit, and we all hope the bus will be making the rounds soon, after a good rest and a nice mulled wine.

Monday, December 21, 2009

Cat of the Month: Man-O-War

To round out a full year of cats, one of my all-time favorites, Man-O-War.
Previously known as Bing, Man-O-War was the first cat I had after moving out of my parents’ house. My roommates and I wanted a cat, we wanted to call it Man-O-War, and after a month or two of looking, we found one at the shelter that fit the ticket. Not every cat, after all, can be named Man-O-War. (And that’s after the jellyfish, not the racehorse.)
Man was black, with some white splashes on his chest and paws. Most of him was a short-hair, except for the tail, which was huge and bushy. The tail was as big as the rest of the cat. And he was long. Standing on tiptoe he could grip the edge of the dining table with his front toes, but not quite look at what was up there.

Man-O-War was one of the smartest cats I’ve ever had. He did tricks. He figured how to get through the hole in the screen to go out on the porch without enlarging the hole enough to make us notice it and repair it again. Once in a while he would get an infected toepad from the sharp ends of the wire screen, and need to go to the vet.

He was allowed a reasonable flow of Bonkers Cat Treats, for which he would stand up to his full height and even take a few steps, like a dog. If you tossed one he’d either catch it or bat it in the air. He knew he wouldn’t get more than one or two for that from me or the roommates, but after an infected paw episode he discovered that our friends would invariably fall for the ‘oh poor me, my paw hurts’ look. Even long after his paw was better.

Man liked riding in the car. If Tim was going to pick me up at work in the winter, or pick up a friend, he’d take Man with him, just for fun. Later when Man's allergies got bad and we had to visit the vet frequently, he would hate to leave the house in the car, but on the way home he’d be up in the windows again, looking at everything go by.

He knew about doorknobs, and was tall enough to reach them without jumping. He could even open them inward, keeping a hold on the knob and stepping backwards. He also knew that I would mind if he sat on the plants. I had never even seen him on my plants, so he had never experienced the consequences. But he rightly assumed there would be some, so he would sit on my asparagus fern with impunity in front of Tim, and skedaddle whenever I walked into the room. This often left Tim with the giggles. I could never figure why this particular plant, which had been doing so well, was now looking so squashed in the middle. It was still doing fine around the edges. Then once, I caught Man O War on my fern, and he saw me looking horrified, and Tim rolled on the ground laughing. It was the very last time the cat sat on the plant, because from then on it did quite well, until I had to move across the country and gave it to my Mom.

When we moved to LA and got Sasha, Man-O-War showed what a gentleman he was. He graciously allowed another male cat into his territory, but more than that, he never stole Sasha’s Bonkers. Man was slim and quick, but Sasha was a ponderous 20-pounder. So in Bonker Races, where we would toss them for Man because he liked the chase, we would eventually give in and toss one for Sasha, who really really wanted one but could barely get his bulk in gear before Man was back to the starting block. We would say ‘this one’s for Sasha’, and toss it (S did have to work for it, after all!), and Man-O-War would just let Sasha go get it. He never ever stole Sasha’s Bonker.
So that was the fine Man-O-War. Don't worry, there's a whole 'nother year of cats in store!

Saturday, December 19, 2009

The Ungrateful Wretches

Poor Natalie. She's been complaining to me about how hard it is to be Top Cat.
It's a thankless job.
The other cats don't thank her at all.
Can you believe it?
They should be grateful there is order in the house.

Thursday, December 17, 2009

Friday Photo Shoot Out: Holiday Decorations

This week's theme is:
My town decorated for the holidays.
"Dressed for Christmas" officially, but 1) I'm not christian so I do a more general holiday thing celebrating the solstice when the days stop getting inexorably shorter (daylight is not going to disappear altogether, thank goodness) and the New Year, and 2) the decorations around town are really quite religion-neutral, with a general, wintery theme. In public displays there are no angels, creches are only at churches, and there are plenty of stars and snowflakes and icicles and lights that are pretty but don't say anything in particular. An exception is made for Santas, who are found at the Christmas Market and in malls all around.
Between the cold and it getting dark so early, I haven't been out and around much. But I did take a tour of the sights this past Sunday, and here are the results. Aw, Santa's hut is closed.

Well, I admit 1:30 is pretty early for the Christmas Market on a Sunday. There should be more people later, checking out the handcrafts and foods for sale.
This guy at the hot beverages stand is not completely without customers, though. At 1°C, a teeny cup of mulled wine is just the thing.

I like the windup toy shop. Made in China, but they do have hopping rabbits that do backflips.

And of course there are Silly Pictures to be taken.

In the warmth of the mall there's a fair amount of decoration.

Santa doesn't have a whole lot to do yet, but it'll be busier later.

They put up the big wheel last weekend. It's a favorite after dark.

In my part of town they've strung some trees with lights, alternating blue and white along this street. These are very nice, but they blink frenetically and I couldn't capture them on at the same time.

Down one of the little streets in the center of Aubière.

Then sometimes you have to wonder what they were thinking.
Blue cones. OK

Lastly, the main tree in Aubière.
It's a real tree, growing at the edge of a parking lot, and I do prefer they decorate it rather than cutting some magnificent creature down just to look at it for a month.

For a peek at Maurice & the Laboratory Rats decorating the tree at our house, click here.
To see the rest of the Shoot Out, click here.
Have a great weekend!

Wednesday, December 16, 2009

Life is an entropy exchange

Just one more word about this evolution thing.
Naysayers often point to the Second Law of Thermodynamics to support their view that evolution can't be true because entropy (chaos, disorder, randomness...) increases.

quick review of the laws:
0 = definition of temperature
1 = conservation of energy
2 = entropy of an isolated macroscopic system never decreases
3 = as temperature goes to absolute zero, entropy approaches a constant minimum

The laws do not at all forbid evolution of complex organisms. They just tell us this added complexity has to be paid for.

OK. A complex organism has less entropy than a simple one. So it's going against the grain to go from simple to complex, and in the case of the magnificent human brain it's just unreasonable.
But hey, we appear to go against the Second Law all the time. Meerly by growing, the simplest bug decreases its own personal entropy.
How can that be?
Well, you have to consider the "isolated macroscopic system". An individual is not an isolated system. It eats. It breathes. It metabolizes. It shits. It has an impact on its environment. To draw a circle around the 'system' here, you have to include the entire planet, plus the moon because its pull provides us with the energy that moves the oceans around, plus the sun because of the energy it send us.
And now there's plenty of room to mess with the conservation of energy and increasing entropy. Living organisms are constantly involved in converting one form of energy to another, and in increasing entropy here to decrease it there. Many developments in body form cost energy (it takes an effort to make an eye, it takes energy to make thick bark), but if that development is more advantageous than costly (finding food more easily, resisting beetles) it will be retained. A development no longer advantageous (like dewclaws) will fade away as its parts degenerate or are co-opted for new uses.
We humans cannot always think of what advantage is being gained, so we cannot explain everything. Sometimes the advantage no longer is one. It can take a long time to adapt to a given circumstance, and when that circumstance changes, the old adaptation may persist for many generations.
The Laws of Thermodynamics have nothing to say against evolution. They just tell us to look at the whole system, and that local differences in entropy even out in the system as a whole.

Monday, December 14, 2009

Change for the better

I was having a discussion the other day about how species change over time. It's interesting how ingrained is the idea that evolution has to 'go' somewhere, that evolution equals progress toward a predetermined goal or an ideal.
Evolution is actually a neutral term. Evolution responds to the environmental pressures of the moment, pressure that can change direction or be reversed. New strains or species are 'better' than the old in the limited sense of being better adapted to succeed in the conditions they've been selected for. To say a species is 'more evolved' literally means it has gone through more reproductive cycles under the influence of selective pressure.
So to people who stand aghast to think humans descended from apes (apes, eww)(whaddya mean eww? we're still apes!), think of this: our closest relatives the chimpanzees are more evolved than we are. Yes, really. From the point at which our branches diverged, they have gone through more generations (because humans become sexually mature later in life), and to show for it they have more changes in their DNA than we do. We have gone a different route, and we have different lives as a result, but don't say we're more evolved.
Bacteria: now those suckers are evolved!

Friday, December 11, 2009

Friday Photo Shoot Out: Weather

This week's My Town Friday Photo Shoot Out's theme is: The Weather!
Here's a tour of the local weather this week, day by day. Saturday, about 4pm
It's just weather. Happens every day. Even in December.
Sunday around 4pm.
Sunday at 5, a hint of clearing in the west.
It's been cloudy lately. It's cloudy a lot this time of year. The weather women keep mentioning rain, but it hasn't rained. Hasn't cleared up, either.
Monday morning from the parking lot at work. Weather photos aren't easy when it's dark when I go to work and dark when I finish there.
It has been fairly warm, though; highs of 13 or 14°C, lows of 6 to 8°C.

Tuesday morning.
Tuesday it looked like it was going to be sunny, for a while.

The wind came up, really whipping the flag on top of the crane just outside our window. It was the only windy day of the week.

Wednesday at 1 pm.
But no, it clouded over again.

Thursday at 1 pm.
And that's the way it is still.

Friday at 9 am.

Only, today it's getting colder. They promise freezing temperatures for the next ten days, with a possibility of snow in the valleys, not just on the heights. Time to get out the wooly sweaters!

Links to this week's Shootout participant are here: http://mytownmrlinky.blogspot.com/2009/12/welcome-back.html


Thursday, December 10, 2009


The thing I hate about small number is you just never know if they're worth anything.
Now, is that a significant difference? 2 is twice 1, after all. Twice!
But if the next number is 183, 1 and 2 look pretty chummy.

And how about 19.8 for n = 4, versus 32.2 for n = 21?
Looks tempting.
But is it any good?
I hate n being only 4. What if some fifth sample has a value of 40, and my little comparison of means is shot to hell? Sigh.

I knew I should have taken statistics in college.

Zebra of the week

It's Thursday! Zebratime!
What do you mean, an imposter?
It's a 4-footed mammal with vertical black & white stripes.
ok, maybe I helped it with the stripes.
but it's still a zebra!
er, an honorary zebra.

Tuesday, December 8, 2009

Ambition and the Scientist

Maybe it's me. Maybe I'm wrong for not thinking big enough. For not having enough ambition.

But maybe it isn't. Maybe the goal of doing research is to get a paper in Nature. Maybe Impact Factor is the most important thing.

I mean, if you aren't doing work that's worthy of publication, perhaps you are a dead weight. If you aren't getting into the literature you aren't getting any recognition and you won't be able to compete for grants that will fund the next round of research. Only: it isn't as if we're not publishing. We're just not publishing in Nature or Science, the biggest journals there are.
What am I talking about?
Oh, sorry.
We've had this one project going on in the lab for several years now, with nothing much to show for it. It was a big collaboration, and our industrial partner was supposed to do all the sequencing work while the two labs gathered samples and interpreted results. Only the sequencing never came through (in spite of our paying for it). So the researchers went their own ways to try to pull something out of the mess, and we're just now at the point of having publishable results for one little arm of the original project. Great! The question is what to do next.
Well, the project was a fishing trip meant to give us new leads on the genes involved in breast and other cancers. The niche we ended up with results for concerns ovarian cancer, but we did indeed get some leads, they can be applied to breast cancer, and there is a wide array of experiments to do to follow up. Fabulous. Now we're getting down to the really interesting part.
Only, these other experiments don't lean very heavily on our magnificent new sequencer. A few of them do, but it wouldn't use the new thing all that much. What my boss wants is a super-sexy project to use the new machine. He saw this paper in Nature where they took one breast cancer, a metastatic sample from the same cancer, and the patient's normal cells, and sequenced everything. Quite a technical exploit. But, although the mutations revealed do suggest leads for further study, it's just one sample. An anecdote.
But it was published in Nature!
So go, underlings, and come up with a fast project that will A) use the new sequencer and B) get us a Nature paper.
I think we should take advantage of the results we're writing up now and do an in-depth study exploring those leads, leaning more on high-throughput sequencing and expression data than originally. We can either gather all the data from the half-dozen different experiments into a single giant paper or we can publish it in smaller but still entirely respectable increments.
But no, the boss thinks that will never get us into Nature. He wants essentially to duplicate that paper he read. He finds it fabulous to show that we can sequence the entire genome of a tumor, and that this is the only way to the Big Time. This is a new fishing trip, and there will necessarily be fish, big and small, in the results. It doesn't matter that everything we've learned from the bit just finished will be put away in a drawer. Or that all of our enthousiasm for taking our discovery to new levels is to be discarded in favor of doing one experiment, over and over and over, until the cumulative data covers the genome 20 times. Or that our lab is in need of diversification in the types of experiments we do, and his project confines us further to a single technique.
My lab colleagues and I don't want to do this project. We think it's pie in the sky. We think it's a technical project, not a scientific one. Yes: It is impressive to sequence a whole human genome. We calculate it will take us 12 months, a million and a half euros, and 6 or 7 people to do it, if there are no problems at all. Will it still be so impressive in a year's time? Highly doubtful. It won't be routine, but it won't be Nature, either.
My boss thinks that we haven't come up with anything else that will get us into Nature. He thinks that our unwillingness (if politically we can admit that the team is in fact unwilling: let's say we're sceptical, or hesitant) to take on this challenge shows a lack of spirit/self confidence/vision/whatever.
I have always had my differences with my boss over his approach to projects with 'here are some tools, what can we do with them?' rather than starting with a biological question and turning your tools to answer it. Perhaps there's a part of me that isn't thinking big enough, but I don't think enlarging the size of the project is ever going to make me start my day with "How can I get into Nature?" And I surely won't ever wake up wondering "What can I do with the machine today".

Friday, December 4, 2009

Friday Photo Shoot Out: My Favorite...

This week’s Friday My Town Shoot Out theme is “My favorite things”.
One of my favorite things is traveling, but I’ve been posting photos from my travels so often recently that I think I’ll give you a break on that. Who needs to see the Torrey Pines State Beach one more time?
Ok, me: that’s who!

And then there’s my faithful traveling companion, Maurice. Who needs a fickle guy when you can just stuff Maurice in the luggage and leave him there if you don’t like his ideas?

My favorite things in my town include messing around in the garden.

Cats on the bed.

Exploring with my brother.

And knitting. Is the color OK, Barry? It’s a disappointing season for greens (unless you’re looking for muddy olive or radioactive lime), so I went with a blue-green mix. Alright, mostly blue.
See you next week!

Thursday, December 3, 2009

What, Thursday already?!