an owl!

G was gently snoring, which is usually reassuring, but was keeping me awake last night.  I swaddled myself in a fleece pullover and a down throw, and sat in the rocking chair looking at the lights over the edge of the deck.  We can see from San Jose up past Mountainview to the north, a continuous sea of lights.  Since it has been raining the air is quite clear and the lights crisp.  From the house below me, there was suddenly an enormous shadow rising up past my window and over my roof.  Wings wide, outspread, and the head in perfect silhouette.  I could see the outlined feather edges on the wings and tail.  A few summers ago I identified the call of a great horned owl, and the size looked to match that species.  Wow.

It's as good as it gets

I'm here at CFSAN (Center for Food Safety and Applied Nutrition, a part of the US FDA) and at NIH this week for some lab work, a Disease Outbreak Detection meeting, and oh, right, Health and Human Services Secretary Sibelius's announcement of the HHSInnovates award.  Yes, Agilent Technologies, CFSAN and UCDavis and the 100K Pathogen Genome Project is the Secretary's Pick.  There will be photos and of course, something to hang on the wall.  24 of us associated with the project celebrated with house wine and spaghetti at a local restaurant, and a jolly time was had by all.  Since I know weI won't be winning a Nobel or even a Lasker award any time soon, it's as good as it gets, we all agreed at the bar afterwards. 

By the way, if you hold a foreign passport, please be aware they won't let you in the building without 5 days to check you out.   Here is Steffen, enjoying the HHS lobby!

Wow! It's like stuffing the ballot box for the All-Stars Game!

I have been working on this initiative all year. The 100K Pathogen Genome Project is a joint collaboration between Agilent Technologies, UC Davis and the FDA to collect and sequence 100,000 pathogen genomes and get the data into a public database. Acquiring this information will allow the rapid molecular identification of food-borne pathogens to vastly improve the security of the food supply, instead of using traditional microbiological methods almost a century old. We are a finalist for the Health and Human Services Innovation award. If you click on the link below, you get to the voting page for People’s choice award. Ours is the center bottom rectangle that says 100K Genome Project. Please go, look around, and if you are impressed, we will take your 5-star vote.


Thanks. It has been a fun ride. I’ll be at the ceremony Sept. 24. Wish us luck!

http://www.hhs.gov/open/initiatives/hhsinnovates/index.html

about those safety door latches on hotel doors

You know, those things that are supposed to catch the door from being opened.  My normal hotel was booked, so I was staying at a Best Western I have not used before.  I was laying on the bed completely immersed in a book.  Still dressed, thank heavens.  There was a sound at the door, then the door opened and the latch caught it from coming open into the room.  I shrieked, and the door hastily closed.  In a bit I peeked out the curtain to see a man looking back at me.  Poor guys were probably (almost) as freaked out as I was.  Stupid clerk gave them room keys to 236, since she recorded that I was in 238.  Well, I wasn't in 238, was I?  Hrumph. 

The peaches are ripe

The kitchen is scented with the perfume of peaches.  Evidently, so are the hills above our house. The fawns, the bucks, the does, the turkeys, the jays and probably every other creature that lives here is visiting and pulling on the tree to get to the fruit.  Yes, the plums and apricots are also delicious, but it is the peaches that brings them flocking to the front yard.  I, too, cannot get enough of the peaches.  Yum.

One of life's obvious lessons (doh!)

My old balance ball bit the dust a few months ago.  I got a new one.  I like to sit on the ball during teleconferences and doing other office tasks.  While I can't sit on it all day - I get too stiff - it makes me feel just a teensy bit better about sitting all day.  So Kitty Guy was on my lap getting rubbed and purring, then something spooked him and BAM!  He was off like a shot.  Not only did he take several bits of my leg with him (nice bruise) but he shot himself off the side of the ball in several. places.  OK, buy a box of bike patches  Blow the ball back up, covering the holes with scotch tape.  Put on 6 patches.  Blow the ball up a little fuller.  Looked good, held the air overnight.  Sat on it awhile.  Got up for tea.  Came back to find my new ball all flabby and shriveled.

Note to self:  one should not hold cats, particularly skittish cats, while sitting on a balance ball.

and the hits on the 100K Genomes Project just keep coming

The e-mails overfloweth.  Congratulations all around, and gleeful lists of web hits are being updated.  There are almost 50 articles out there after the press releases went out yesterday, although some of them are re-prints posted to a different site.  The report posted to Genome Web News is the 2nd most viewed and the 3rd most e-mailed.    But the best result is that offers of isolates and other help are now flowing into UCD.  After the first 1500 isolates are sequenced and polished, it really will be like looking at pathogen genomes with the Hubble instead of binoculars, as the Director of the FDA suggested. 

More on the genome alphabet soup

Our project to sequence the genomes of 100,000 pathogen bad boys and put them in the public domain has finally gone public.  Amazing how many months it took to put the press release out there.  100K Genome Project Access to these DNA sequences should allow us to construct molecular assays to identify food-borne pathogens.  That will be a significant advance from using the bunny antibody techniques for serovar identification that were developed early in the last century and still in use today.  If the identity of a food-borne pathogen can be determined in hours and not weeks, that will trim weeks off the time it takes to trace-back the source of the food poisoning to the farm or factory.  Our next meeting is in two weeks, and we will all be proud to have this out there.

It's a fine thing for my company to sponsor.  My manager offered me this position in the Food Team a couple of years ago.  A few months after that, his father sickened and died from food poisoning in a few days.  It's not always all about the corporate bottom line.

Batter fried onion rings

Yesterday I drove past Pleasanton CA over 80 east toward Davis.  I try to leave mid-morning when the commute traffic has calmed down, but there is still a hilly part where traffic is a bit slow.  I saw a few motor homes in the slow lane, then a SHAVE ICE vendor being pulled by a truck.  Another SHAVE ICE truck being pulled by a motor home.   A HOT DOG truck was ahead of that.   When I passed the Batter Fried Onion Rings truck, I realized that I had just passed the fair grounds in Pleasanton and the fair was over yesterday. 

The mockingbird chicks have fledged

With the windows open, the background calls of Tshick tshick tshick by the parents patrolling the yard is rising and falling as the adults fly around.  Louie-cat proudly brought one of the fledgelings to me, Louie and the baby crying out together.  I retrieved the gift, propped it onto one of our tallest bushes, and it was gone when I checked on it a few minutes later.  When I was at the kitchen window fixing tea yesterday morning, the fox who lives next door darted across the grass to get to the water in the little fountain next to the house.  The adult mockingbird was in hot pursuit, pecking at its back.  It looks like a lot of work to raise a family of chicks.

Five kinds of tea

I walked down the street in downtown Atlanta with some colleagues today for lunch.  We went to a thriving salad-and-sandwich kind of place for a marvelous lunch.  They had five jugs of tea AND lemonaide.  You gotta love being in the south. 

Home again, jiggety jig.

I'm tired, I'm home, I'm covered in cat hair all over my black skirt.  I'm here tonight and tomorrow and then it's another airport.  Is my talk done?  No.  Do I remember what I promised to talk about?  No.  I can look it up on the airplane, can't I?  So I have laundry, two more fruit trees to thin, and the rest of the garden to dig up.  I'll actually have a week and a half at home to do the latter before I take off AGAIN.  Sigh.  Makes me tired to think of it. 

How to tell when traveling in the south

I was driving to Richmond VA to attend my aunt's memorial service and stopped in a drug store to pick up a drink.  Lipton plain tea in a bottle?  Not a chance.   Sweet tea and Extra Sweet tea?  Two rows of each.  

The service was lovely.  There were tears in her memory, but we are a restrained bunch.  Two daughters, two granddaughters, two grandsons, along with friends to respect her memory.  Uncle Jim looked old, frail, but surprisingly strong after his recent stroke.  There is a military cemetery outside Richmond, green rolling lawns - a peaceful place.  We all needed closure after a rather bad ending to her life, which in any event, does go on for the rest of us.

We needed to sit in the room for hours together, chatting of this and that and recent events.  And so we did.  Blood is indeed thicker than water.  Uncle Jim was so pleased to see each of us, as we were glad to have him with us.

Stand-in Sugar Daddy Duty

My management team bankrolled a locally-produced documentary about insuring the safety of the food supply, and I am here on campus for the reception and viewing the film.  It was lovely.  I got quite shiny suit-sleeves rubbing elbows with the deans and directors who came around to thank my company for the funding.  I met the producers, and sat with my professors and A's charming and well-behaved young daughters.  I was asked to speak briefly, and I told our story about how we transitioned from making test-and-measurement boxes to creating a food team to apply those solutions for assuring the security of the food produced by local agriculture.  While hiring his team, P's father contracted food poisoning and died within a few days, so food safety is not only a company pursuit, but an up-close-and-personal priority for our team. 

fast forward a year later

Last spring one of the terrible cluster of tornadoes that hit Missouri hit STL, the airport a few miles from my childhood home (where a parking garage now resides)    I watched the big glass arches of the terminal go up as a kid in early elementary school. Last time I was here There was still a LOT of plywood. Now it is light and airy again with new glass. Even better are the new corridors to the gates. Gone are the low, dark suspended ceilings that were oppressively close to my head. The support struts are opened up and they and the corrugated metal roof are painted cream. A false ceiling of big pans of glowing lights give a sense of openness. What an improvement!

P.s. A clue to the nature of this blue collar city is in the news shop. One rack of paperback books, 4 racks of magazines, and tens of racks of merchandise. One suspects the literacy rate, scientific or otherwise, is less than 29 percent.

Alphabet soup and the Pathogen Genome Project

Six months ago there was a meeting of 25 scientists in Brussels. This week there has been a meeting of 100 scientists to discuss accumulation of the various sequencing outputs into various centers. Most of these data repositories are known by a collection of initials and are part of some agency of some government somewhere.

From left:  Paul, Food Team Manager, Agilent Technologies; Eric Brown, Division Director, Microbiology, US FDA; Steve Musser, Director, Office of Regulatory Science, US FDA; Marc Allard, Microbiologist, US FDA; Bart Weimer, Professor and Director, Pathogen Genome Center; Steve Royce, Manager, Americas Food team, Suf Al-Khaldi, Research Scientist and Food Outbreak Investigator @ US-FDA, US FDA, and me.

PZ stood before the first break and announced U CA Davis is starting an initiative to collect 100,000 cultures AND genomes of pathogens over the next few years, and that these would be publicly available.  There was silence followed by a smattering of applause. Later we figured out this was the length of time for a collective "Oh #*!!  That means my 10,000 cultures I was going to build the rest of my career on have gone the way of the buggywhip" realization.

This is Big, my friends, BIG. This changes the game in place since the days of Louie Pasteur. More in another post. 

Scientific Literacy and the teaching of science

I have been indulging in my favorite airplane activity: catching up with recent issues of the journal Science. Last year the journal started a series of essays on inquiry based instruction. I learned lab science the old fashioned way - the way it is still taught - the lab book instructed you what to do and how to do it. You did it until getting the prescribed answer and then wrote the lab report. That IS what science is about, right?  The 'right' answer?

So in the first of this year's essays, a group of 5-year-olds were given a box containing a varied mix of seeds, nuts, pebbles and shells and spent weeks investigating "what is a seed"?  Open ended. No right answer. Fun.

The article opened with the assertion that 28 percent of US adults are scientifically illiterate. Ya think?  And that includes some presidential candidates. Huh.

Chocolate at the Robert Mondavi Institute for Wine and Food Science

Saturday I collected on my Christmas present - a seminar on chocolate!  We drove up Friday night, so we easily arrived by 9 a.m. for registration.  Chef Lionel Clement built a chocolate sculpture from pre-cast pieces.   He also answered questions while he worked - I don't know how he did THAT.  Fun.

In the afternoon there were a few presentations and a chocolate wine pairing, which was not to my taste at all - flavored bon-bons are not good choices for wine pairings.  Carl Keen talked about flavenoid research, and I really want to do some further reading when I get some time.  Dove dark chocolates is the take home message.  The flavenoid concentration depends on how you prepare the chocolate, and Dove seems to hang on to the most of them.  Also the active flavenoids in tea appear to be converted into an inactive form the longer the tea sits at a higher temperature.  I will experiment with brewing my tea at a slightly lower temperature to see if I can take advantage of this information.  I may as well take health advantage of my addictions.

Woo Hoo! New toys on the way

My BlackBerry crackled at just the wrong moment last week, causing me to misunderstand a Not instead of the Very Important, and miss a teleconference.  I told said boss the speakers were too noisy.  Get an iPhone, he offered.  And a new printer with a fax (so I don't get customers to send my things to him instead) and a scanner.  Welcome to this century!  So if you tell me the best apps, I'll appreciate the advice.

Fish Barcode Of Life

http://www.fda.gov/Food/FoodSafety/Product-SpecificInformation/Seafood/DNAspeciation/ucm266440.htm
Please visit the FDA Fish Site for just a minute.  There is a Barcode of Life effort underway to post a little bit of the DNA sequence for EVERY organism on the planet.  Considering we have not identified them all yet, this is pretty ambitious.  A global offshoot, known as  FishBOL, http://www.fishbol.org/ collects the Fish sequences. I am working with Jon, and he does the work for this site.  Someone sends them a frozen fish, and it gets Authenticated by an ichthycologist.  Jon photographs the right side of the fish with a color bar.  Then he removes some tissue from the underside of the fish, where it would not show in the photo.  Then the fish heads for the Smithsonian, where it is stored with a code (Vouchered).

So, what happens if you have several individuals of the same species of fish and you find out the DNA sequence is pretty different even though the fish looks the same to the expert?  Some times it gets reclassified as a new species.  That is why it is so important to keep the fish in the museum.   You can get it out of storage, check it all out, and reclassify it.  Pretty cool, huh?

There is also an effort underway to do the same process with zoo animals and bush meat confiscated by customs.  You want to volunteer to authenticate, photograph and voucher a tiger?

Illumination in the Flatwoods

My dear friend lent me this book Saturday, Illumination in the Flatwoods by Joe Hutto Illumination in the Flatwoods A season with the wild turkey http://www.amazon.com/Illumination-Flatwoods-Season-Wild-Turkey/product-reviews/1599211971/ref=sr_1_1_cm_cr_acr_txt?ie=UTF8&showViewpoints=1  It is the story of a naturalist who spent a summer with a flock of wild turkeys.  He lives in the flats of northern Florida, and I have spent time roaming those forests during the years my Grandmother lived in Tallahassee when I would go walking.  I have a flock of male turkeys who drink from my birdbath and often shelter in the shade under my little tree.  So when I got home and opened this book, I stayed glued to it until I finished it later that evening.  I have observed many of the behaviours Hutto describes, but his beautiful descriptions put this all in a new light.  If you are even a casual birder from your window, this is a riveting, fascinating book.