Antimicrobial Resistance

Occupy UC Merced

2012-02-09T18:18:00.001-08:00

I have two thoughts about this:
1. At most universities there are students who cannot simultaneously afford housing and tuition. I have known people who lived out of vans, and college offices. It is pretty easy to do since shower facilities are in the gym. The "Occupy" movement provides a social construct which makes being a homeless college student acceptable.

2. I rarely see students near the five tents pitched in the little cluster of trees. This photo captured the most students I have ever seen occupying the "Occupy" site. I never see stuff. When people camp, there is always stuff. So maybe the students are spending time at home and sleeping in beds. I hope this is the case.

Post-modern Pet

2012-02-07T00:07:00.002-08:00

Waiting is a wordless vacuum. I have nightmares about waiting. Anxiety stretches into infinity in my dreams and in my waking. The knots in my back, stomach and chest are reminders even when my mind becomes occupied with the essentials of existing, doing my job, or working on my house. Someday I will find out whether I will be a scientist when I grow up. I feel like when I find out either way that I will disintegrate into a mud puddle: flat, amorphous and wet, for a few days and then be able to go on. In the meantime, I am preparing probably the most expansive paper of my (hopefully) early career, and reviewing NIH grant applications. Those efforts exhaust whatever remembered shreds of language are left inside of me.

So I think I will start blogging with pictures instead of words. I have conquered words. This does not mean that I can make them sit up and beg, roll over or jump through hoops. They are still untamed, but what it does mean is that I know I can survive them, use them, and better yet, enjoy them. I can appreciate Terry Pratchett's wordplay, and pick apart grant applications, and geek out with Marie over the endless depths of Biblical language and imagery in conversations that may or may not turn into discussions of the insanely dark humor of Twin Peaks, the best television show ever made. More importantly, I can write now. Well enough to get by anyway. But pictures are more difficult at this point, so I will work on them for a while. I suspect that they will start out bad and get better. That is the hope anyway.

My first is called "Postmodern Pet". I travel too much to have a real pet. Instead of finding it abandoned at the end of the dead-end road I grew up on as a child, I found this one in a heap of junk at a flea market. I got a key for it and found out it works.

My New Favorite Band

2012-01-16T08:54:00.000-08:00

<p>&amp;amp;amp;lt;p&amp;amp;amp;gt;&amp;amp;amp;amp;amp;lt;a href="http://music.troubledtunes.com/album/the-intemperance-e-p"&amp;amp;amp;amp;amp;gt;The Intemperance E.P. by John-Ross Boyce and His Troubles&amp;amp;amp;amp;amp;lt;/a&amp;amp;amp;amp;amp;gt;&amp;amp;amp;lt;/p&amp;amp;amp;gt;</p>

Jim Crow

2012-01-11T18:56:00.000-08:00

Jim Crow passed away last week. I never met him; he had already surpassed the average life span of humans before I even thought about becoming an evolutionary biologist, and there was no reason for me to intrude. And it may be weird that I think of him as a friend, but I do, because he and Kimura wrote math about everything, and they did it right and they included math about bacteria as bacteria and not as single celled eukaryotes. It was all well thought out. And when I have come up with crazy ideas about the way things REALLY are, and so many scientists condescendingly disagree, I have almost always been able to find math of theirs that credibly backed me up and eventually I have gathered the data I needed to bring scientific thought a little closer to a truth that their math predicted years before. I am grateful to Dr. Crow for simply doing good and honest work, and then writing books about it that made it accessible to students. His work has given me the confidence and intellectual backing I have often needed to be the iconoclast of a scientist I so often am. He was one of the good ones.

Blogging Sabbatical

2011-12-12T15:57:00.000-08:00

In the beginning of my blog I had two reasons:
1. To be able to share ideas about antibiotic resistance.
2. To improve my writing skills.

For me it has actually accomplished those purposes, and I am now getting asked to write a lot of material that can actually get published by someone besides me via blogger. I am also writing a lot of manuscripts for peer review. I am finding larger audiences through those than here and those publications are certainly more prestigious. So I think I am done blogging for a while, but I reserve the right to return whenever the whim to do so suits me.

Tools of the trade.

2011-12-11T09:16:00.000-08:00

It is autumn in Merced. The ice cream trucks have stopped running and the air smells like soot from the fireplaces placed once again placed on active duty. When the wind blows, showers of leaves flutter to the ground, much like snow does in some places. When light falls across someone walking through mixed shadows, it often looks like water or salt spilling down in front of them.

The semester is over. I am starting to mentally gear up for the teaching I will soon do. I craftily arranged my schedule so that I would have a full calendar year without teaching. As I head back to the trenches, I am worried I have gotten rusty. It is not so much that I doubt my ability to stand up and teach the material I have taught so many times before; it is the concern that some of my techniques have become obsolete. I am particularly worried about my sense of humor.

I believe that humor is essential to teaching, if for no other reason because it is so boring to teach essentially the same material year after year. Humor entertains the professor and lets her know for at least a few moments that she is accomplishing something other than torturing the students. It wakes them up, and makes their minds a little more receptive for at least a a few seconds. But humor is a tricky thing. It doesn't translate well from language to language usually. What is intended to be funny, can come off as offensive.

There is a sort of humor that emerges in people who experience acute physical suffering for extended periods of time. It is black, and to those who do not know what they are looking at, it may seem cynical or even frightening. To those who do understand, it is an expression of joy and hope even in miserable circumstances. It is a mark left on a person even when their suffering has ended. People who have that sort of humor, usually connect with people who share the same humor and with people who can see that it is humor. It is a strong indication of certain personality traits: patience, tolerance of physical labor, tolerance of rudeness, tolerance of the different ways in which people experience life, and an ability to find joy and games anywhere.

Among those who understand what they are looking at in such a person, it is bad form to ask up front about the suffering that brought about their particular flavor of humor. That question would be a request for a recollection of the worst times in a persons life, but if you get to know someone well, the topic will come up. It has shaped the character of that person. He cannot talk about himself in great depth without it coming up at least a bit.

With pretty certain anonymity, I will share an example. I have known a certain girl with scoliosis since she was seven. We clicked immediately. She drew the funniest pictures I had ever seen, but they made most people upset, at least a little. In her child's hand, they were entirely accurate depictions of people. She drew bald spots, round bellies, frowns on grumpy people, messy hair, crooked noses and so on. There was no malice in it. They were drawn out of joy, affection, enjoyment of the goofiness that accompanies humanity. She honestly didn't even understand that she was broaching sensitive subjects. And really, how could she? She had a crooked spine and hunched shoulders that painfully disfigured her all the time. There was no room for her to be sensitive about her back. It certainly wasn't sensitive with her. And the insensitive comments of others barely registered by comparison. They were nearly nothing compared to the pain. She could either be miserable all the time, or take what joy she could find.

When she was twelve, she dressed as the Hunchback of Notre Dame for Halloween. That made almost everyone but herself and her mom really uncomfortable. When her mom told me, I was concerned, but when the girl told me herself, chuckling and smiling like it was the best joke ever, I got it. She had back surgery scheduled in December, her spine would be straightened, the pain mostly stopped and like a Halloween costume, she would shed her suffering. For her, Halloween was a celebration of metamorphosis. She wore that particular costume because she was ending that period of her life with a bang.

Most of my students, from first generation, blue collar, immigrant families have shared that sense of humor, and they have taken comfort in having a professor who could joke with them at that level, subtly, and in the middle of lecture. But the student body is changing. It is becoming higher class as the reputation of the university grows. I gave a lecture a couple of months ago, and my humor fell flat. The students looked at me like I was a frightening and un-sympathetic person. I used jokes that have reliably yielded smiles and bright eyes for the past six years and they flopped.

So through this holiday season, I am trying to hone my humor of trivialities, pop culture, picnics by the lake and noodle salads: in short, connect with people who find misery the least likely place for humor, instead of one of the most likely. I am nervous I may not reach proficiency in time.

The wonders of amoxicillin

2011-12-07T15:49:00.000-08:00

This is possibly the lamest blog post ever, but to me it is significant. For the first time in nearly thirty years, I am taking amoxicillin and I am getting well. At this point, amoxicillin is one of the neatest drugs we have. It cures Streptococcus pyogenes, the causative agent of ear infections and sore throats (ie strep throat). Although S. pyogenes has been treated with amoxicillin and its close relatives for over 70 years, it has never become resistant. It just doesn't seem to have that potential, so amoxicillin can keep on curing it indefinitely.

Almost every other microbe is resistant to amoxicillin. This may seem bad, but this also means that amoxicillin doesn't usually decimate the bacterial flora of the gut, which is necessary for good health. And, to make make matters even better, forcing bacteria to become or remain resistant to amoxicillin actually seems to help them remain susceptible to other antibiotics. This means that for anything that isn't S. pyogenes, other antibiotics may be more likely to work if the strain is amoxicillin resistant. So even when amoxicillin is being prescribed as a placebo for viral infections, it is still probably doing good by helping eliminate other types of antibiotic resistance.

In medical treatment locations, there are a lot of signs out this time of year suggesting that you probably don't need an antibiotic for a cold or flu, but I really can't see a down side to taking amoxicillin (unless you are allergic to it), so if you think you need an antibiotic, ask your physician for amoxicillin.

Street Pajamas

2011-12-05T16:52:00.000-08:00

I have fallen in love with the idea of street pajamas today. According to The New York Magazine, it is a new fashion trend. In my hands, it would be a dangerous one. I would rather wear pajamas than almost anything else on earth. At clothing stores, I find myself longingly craning my neck towards the pajama rack as I try on less comfortable but more socially conscious attire. When I come home and retire from social consciousness, I pull on some pajamas.

I am sick today, working at home, in pajamas. I blame the registrar. I decided to be socially conscious and a good citizen and coordinate a seminar series this semester. There are a few first year graduate students required to attend for credit, but mostly it is an open seminar to be attended by any and all who are interested. We are out of space at UCM and so the registrar moved the seminar into a small room designed for thirty, instead of the more spacious accommodations we usually have and he justified the move with the low number of students enrolled in the seminar. But lately, we have had anywhere from 40-70 people attending, and I just don't think the ventilation is designed for that many people, so I keep getting sick every weekend. (The seminar is on Friday.) I approached the registrar a few weeks ago with the problem and he was unhelpful....and rude. And I found myself involuntarily listing off the various pathogens that can cause mild food poisoning in my head as I stormed away, not that I would ever try any of them.

I have since replaced those ideas with happier thoughts however. I would be okay getting sick if I could go to work in pajamas. It would be a fair trade. However, as Merced is about 15 years behind fashion in any place that is fashion conscious, it will be a while before I can respectably do so. However, there is nothing but my own inhibitions barring me from disrespectably doing so, and that is something worth thinking about. Particularly if i ever have to go see the registrar again.

High Altitude Chemistry

2011-11-27T22:24:00.001-08:00

I hosted Thanksgiving this year. It was the first since graduate school, (which didn't actually really count since my roommate's mom ordered a precooked Thanksgiving feast from the grocery store for us, bless her). We stayed in Yosemite, and considering that use of the facilities required intellectual pursuits we had a sort of science retreat. (There are major perks to having blood relations, and in-laws and their relations who are intellectual giants.) We came up with ideas about what aspects of laser hair removal need improving, new ideas for green technologies and what they need to progress, the benefits of becoming adjunct faculty, and we also discussed literature, the collective subconscious, music, and creativity. I named the event a "High Altitude Chemistry Workshop" and I wasn't sure what that would end up meaning, but due to the preponderance of large rooms furnished with numerous twin sized bunk-beds in the place we stayed, that meaning was largely limited to intellectual and culinary activities. (We'll see if anyone is supportive of me ever hosting Thanksgiving again...)

Among the pseudo-intellectual activities, Tom taught me how to tie sutures on a turkey. Were it possible for the skin to knit together, it would have had the absolute minimum amount of scarring possible. Tom is a rather good dermatologist after all. (He is already planning how to suture a turkey even better next year. )

We also pressed cider from apples collected in the orchard of the adorable Apple-Blossom Inn. Candy, the owner, let us come and pick the apples she wasn't going to get to in exchange for trying our cider. This seemed more than fair and the cider turned out well, so I hope she felt that way also.

And over the break, something good happened....good beyond the pleasure of being with family and friends....I got evidence that my career is starting to catch up with my science. I got asked to start reviewing grants for NIH. This means:

1. At least someone at NIH is aware of my existence.

2. I will get to read some grants that others have written.

3. I will get to hear the discussion of those grants.

4. I will probably start writing more fundable grants.

I have heard of reviewing opportunities being used as an on the job sort of mentoring in grant writing for the mentor-less who do good science, but haven't had much success getting their work funded. Regardless of whether that was the intent or not, I plan to use the opportunity that way. Since I have some approaches for using antibiotics that I'd like to test, and that seem reasonably likely to work, the timing for this is perfect.

Subversive Sanity

2011-11-21T10:37:00.000-08:00

I have started a wall of subversive artwork down the hallway from my office. I don't quite remember, but I probably started it the day a certain faculty member pointed out that I do not serve on loads of academic senate committees and suggested that I serve on more. I used to serve on lots of them, but the end action was always to write a memo to the dean, which she never acted upon and probably never read. Not much temptation to carry on with futility.

The wall was really started by a certain nameless friend of mine who kicked a hole in it one day when he was mad at the administration. Those of us who work in that hall eventually got tired of looking at the hole (it was lowering morale) and so someone covered it witha a children's coloring book picture of a mouse playing tennis. After a few years, I got tired of the mouse and more frustrated with administrators and found an outlet...subversive artwork. It goes well with the bootprint and it resonates well with many other faculty members.

I have loosely followed Occupy Wall Street, and I don't quite get it. It is roughly organized by a man who sells shoes and a magazine. He lives in a large home on a large property, but he says he hates capitalism. He sleeps in a warm bed and encourages others to sleep in a park. I would say that he probably means well, but I think his actions speak for themselves. There is a sense of the French Revolution about the organization of this; the revolutionary leaders didn't hate the concept of having elite, but they wanted to change who the elite were.

What I do understand about Occupy Wall Street is that at least some of the people who have camped out in parks are tired of feeling powerless and want to find a voice. Oh, how I understand that. And for a while, the movement has probably helped fulfill that need. But I don't know if it will give them the result they want. If capitalism is torn down, other varieties of elites will rise; after all there is social and economic stratification in China, the last and greatest stronghold of communism.

So I hang funny pictures in a hallway and other people protest in parks, and I think such outbursts do ameliorate acute frustration as it arises. But I have never found a feeling of power from subversiveness.

Recently, I did have a brief moment where I felt a little power. A friend of mine recently returned from her son's funeral. He had been shot in the head by his girlfriend when he tried to break up with her. My friend has been fairly stoic about the whole business. Her son had been living a dangerous lifestyle for years and she knew it wouldn't end well. She doesn't want to talk about it, but I asked her how she was doing, and she cried some and I talked to her some and mostly listened and she felt cared for and loved and not so alone.

Intelligent Design

2011-11-15T21:53:00.000-08:00

We had Steve Jobs, Frank Lloyd Wright, Alexander Calder, and John Roebling who were great....truly, but by and large America isn't known for it's design. I hypothesize that this is because most of us come from poor immigrant stock and to our ancestors, design was probably frivolous. But still.....I learned an appreciation for good design and that America doesn't have much good design as a child, because whenever my dad would try to repair something that had broken, he would usually start saying " Bad design, BAD DESIGN! And the volume and frequency of that statement would increase the more frustrated he got.

It is because of my Dad really, and Laura that design was and is such a part of my family. My dad is more interested in mechanical and digital design, functional design. Laura is more interested in designing form. Utility is required by her as well, but so is aesthetic. My dad as an electrical engineer designs many things, and Laura as an up and coming graphic designer in NYC designs many things.
But Tom is sort of a designer too. Surgical incisions are as much an art as anything else, and to minimize scarring the surgery must be well designed. Marie too designs essays and stories. James, music. Michael, games. Carl, pranks.

I have never felt that I fit in the designer category. I can solve design problems. For example, Laura approves of my house. She says I have a cute life and likes how I have organized my home to meet my needs. She also likes the colors and aesthetic choices I have used. But I don't think I could design for a living. After all, six and a half years in, I am still trying to work out what I would like to do with my worse than awful bathroom. And I am getting close. There are only a few choices left to make, and then it will all come together pretty quickly.

With science, there is sometimes design involved. Some experiments are utterly obvious. In fact, most are, but a few require some design. I can count on one hand the number of experiments I have done that I would say required any sort of advanced design. And I do count them from time to time because they are what keep me hooked on science. The needle in the vein. Especially when things are not going well. And things have not been going so well lately. Nothing horrible, just disappointments, frustration, and anxiety over tenure, problems in the lab.

A couple of weeks ago, I couldn't take any more, and so I took advantage of a peculiar aspect of femininity; women are hardwired to feel better when they shop. (I could explain the evolutionary reasons for this, but I won't. They aren't important right now.) So I drove up to Turlock to shop a bit and eat dinner at Chipotle and feel better so I could be productive the next day, and it worked out ok. A girl making my vegetarian salad (guacamole!) asked how my day had gone and I told her it had been truly horrible. When I got up to pay for it, the guy at the register looked at me like I was absolutely beautiful and told me not to pay for my meal since my day had been horrible. And I didn't and he didn't even do anything weird or awkward...he just let me eat my salad. And then I didn't find what I had been looking for while shopping (which was fine since the real intent was retail therapy), so I didn't spend much money, felt a lot better, and went home.

The problem with shopping is that it doesn't last very long, so about a week later, I was in the same funk again and went to the next step beyond shopping: yoga style meditation. As I dissected all my sources of anxiety, I came upon two that were at the heart of it.
1. I couldn't figure out how to clone the genes we needed in the vector we needed.
2. I needed a way to translate the past decade of my research into something clinically applicable. (If I keep saying this is the point of my work, I needed to show how that should be done.)
And I took up the matter with God (which is the extent to which science and religion intersect in my thoughts and beliefs.)
And a day later I figured out why we don't need to clone the genes I have wanted to clone and a better, simpler, more elegant approach to those experiments.
Then later still, I figured out how to design antibiotic regimins that will minimize and possibly reverse the evolution of resistance. It may take a little while to show that it works, but I am nearly certain it will. From my vantage point, and after a decade of studies, it seems obvious.

Life is starting to seem good again. And maybe, just maybe when/if this approach really enables us to design sustainable prescription practices, I will join the ranks of the designers in my family.

Melting pot

2011-11-07T22:09:00.000-08:00

The thing about biology is that it is a melting pot. It is supposed to be the study of life, and it is, but in a broader sense than most realize. Life encompasses so many things, art, literature, relationships, chemistry, physics, philosophy.

Take evolutionary biology for example. Religious fanatics hate it and some evolutionary biologists hate religion and between them, they make a fuss about it and drag Charles Darwin through the mud. They often do this with his book On the Origin of Species, which they have clearly never read because it is dull and non-controversial. It is good science, sound logic, and thorough and I never could quite see where all the fuss about it comes from.

Until I learned about Ernst Haeckel...... He was a biologist, naturalist and philosopher. An awfully lot of his biology was wrong, but he invented a lot of terms for the different parts of developing embryos, so he has left a mark in that sense. Some of his philosophy has stuck with us too. He was strongly influenced by the poetry of Goethe. He often began his writings by quoting poetry from Goethe and a lot of the ideas in his biological work seem to have been directed towards giving scientific proof for the ideas in Goethe's poems. For example, Haeckle draws trees that attempt to show the evolution of man and they all point towards man being the supreme being on the earth and all of nature conspiring to make him so. He also spent a fair amount of time fueling arguments between religion and science that sound much more like those today than anything in Origin of Species.

But Haeckle wasn't the only biologist to have his work influenced by writers. The movie GATTACA came well before the first sequence of the human genome and now just like in the movie, healthcare companies are starting to sequence their patients. Perhaps the writers of the movie had foresight or perhaps they changed the direction science would move in.

And in one of the follow-up books to A Wrinkle in Time there are people regenerating human body parts with some sea-star derived technology....We aren't there yet, but with all the stem-cell work going on, it is a direction biology is pushing in. To what extent authors simply understand human nature and to what extent they shape technological advances is difficult to know.

So as I read Hellboy over the weekend and fixed my car and hung light fixtures and changed out light switches, and planted bulbs for the spring, it seemed all like it was well within the line of duty for a biologist. Next weekend, I will take a friend and her children to a natural science museum and tell them about life, the universe and everything, and perhaps I will feel like a biologist as I do that too.

Fear Factor

2011-10-31T15:43:00.000-07:00

I used to be afraid of hanging light fixtures and not afraid of the dark, but after (almost) all the light fixtures in my house stopped working during past couple of weeks, I decided that living in the dark is scarier, so I hung three light fixtures and installed two light switches.

I used to think I was afraid of the tenure process, but after submitting all of the materials for tenure six times, I just want it to be over. I don't think I have to submit any more, so it might be close to over.

If I watch the first ten minutes of Texas Chainsaw Massacre, I will be afraid of going outside after dark, so I don't watch Texas Chainsaw Massacre....at all, ever.

I am still afraid of my crawl space, but after climbing under my bed a bunch of times to plug stuff in, clean out dust bunnies and adjust the supports under the box springs, I think probably the crawl space would be not too much worse.

I am scared by the amount of writing I have to get done in the next two months. There probably won't be much time for blogging, or much to say. I am writing book chapters in which I pour out all of my accumulated knowledge and views about antibiotic resistance, and a bunch of manuscripts where I tell every new story I've got.

And I am scared that the essence of all of my work and knowledge can probably be condensed down into less than two hundred pages.

And so instead of dressing up as a ghoul and frightening small children, I will be home tonight writing like crazy, and facing the things that scare me most.

Happy Halloween.

report

2011-10-14T12:10:00.000-07:00

Barry Hall asked me to report on the first Bellingham Research Institute retreat, since I hosted it and so I suppose I shall. Here goes.

On Friday of last week, we had a meet and greet with Barry and my graduate students in the midst of my lab being audited for biohazards. Apparently, there are new rules that declare us unable to receive packages until our labs get audited and we needed to receive that package. I had been audited the week before and done pretty well, so it seemed silly but un-intimidating to be audited a week later. I hope I don't have to get audited every time a package comes. Barry was favorably impressed with my students as well as the view from my office. He and I attempted to get some R programs working on my computer. We couldn't, and wound up installing Xcode on my computer in an effort to help. However, the R programs still don't work. I'll figure it out eventually I am sure.

Friday night, Barry, Sue (his wife) and I drove up to the Yosemite Field Station for the weekend. It was very nice once we had cleaned out the previous tenants old food that he left behind (iccck). (I will ever after go up a day early to make sure there are not old flowers or halves of limes left behind on the counter.) We ate fondue and discussed adaptive landscapes until one in the morning.

Saturday, we went to Mono Lake, which is a strange place with formations of mineral deposits that came from springs beneath them bubbling up into the lake. Then the lake level dropped and the formations became visible. There were birds, flies and brine shrimp in the lake. Thankfully the flies were a different sort that hang out on the water and don't like humans or sandwiches. They sound like sparkling water when a whole swarm of them flies off. They are neat. We discussed ways of merging adaptive landscapes and plotting antibiotic resistance phenotypes.

Sunday, we walked through the Sequoias and as it was a bit strenuous and at 6,000 ft, we didn't talk so much.

Monday, we packed up and came back to Merced and left the field station in better shape than we had found it. We met with my student Christiane and gave her the opportunity to explain adaptive landscapes. She did quite well. Tony Dean called that night and was excited about some amazing results he got. He said to consider myself hugged and kissed and everyone celebrated his good fortune and excellent research.

Tuesday was the real work day. Since it is impossible to book a meeting room all day at the university as we are low on space, I transformed my house into a meeting spot, by taking down all of my pictures and applying removable adhesive white-board to my wall, removing unnecessary furniture and providing everyone with paper and pencil, and lunch at the appropriate hour. Kristina Crona, Devin Greene, Barry, Christiane and I attended. We discussed the mathematics of adaptive landscapes, their uses and how we intend to get money to study them. We have a few plans in place now.

Wednesday was the activity part of the retreat and Barry, Sue and I went into Berkeley and San Francisco for the day. Our favorite stops were The Cheese Board and The Slanted Door. Barry also liked the large tropical aquarium in the CAS Museum in Golden Gate Park. So did Sue and I. And then it was over and Barry and Sue left Merced, and in their departure, they also left bit of an empty spot in a very tired host of the first Bellingham Institute Retreat.

Pick your Poison

2011-10-02T22:18:00.000-07:00

One of the most surprising things to me about becoming a biologist was learning that the beauty of life scales down to submicroscopic levels and is even in the darkest places. It does not stop when the particular pieces are hard to see. If we could see inside of subatomic particles, I am convinced their beauty would rival that of mountain pools and light glittering through aspen trees.

Wheels are a good example of molecular beauty. There aren't so many of them in nature. They are actually not a very good way of getting around. Usually, you have to make roads for them so they don't get stuck and they also mow things down and smash them. There are only a couple of places where wheels exist naturally. One is in the flagellar motor of bacteria. A little wheel spins around and around to make a tail spin so that bacteria can move through water. Another wheel is the molecule "ATP Synthase". As scientists worked to figure that one out, the wheel presented itself as something that was as magical and beautiful as any story. It could be from a fairy tail, but instead of spinning straw into gold, it spins electrons and phosphate into ATP, the currency that our cells depend upon for energy.

There can also be exquisite beauty in death. There are a few times that I have been acutely aware of how fragile life is, like when a van door flew open and my little brother wasn't wearing a seatbelt, or when I fell off of a waterfall, or when I was catapulted from the back of a four-wheeler through a very thorny tree and then somersaulted down a very steep hill into a stream of water. More often than that however, I have been impressed with how robust we are. Survival kicks in: I slipped my arm around my brother before he fell out of the van, I positioned myself feet first down the smoothest part of that waterfall, and after falling through air, I landed fairly gracefully and tucked and rolled quite athletically down that hill despite a complete absence of gymnastics training. And outside of me, even when my grandmother was ready, willing, and waiting, that it still took her body a month to shut down completely. We are born to survive. It is what we do. It is why euthanasia is a crime, and why a last meal is given before the death sentence. Our most basic instinct is to survive, and out of that comes respect for life.

But life has also evolved implements of death and some are elegant and beautiful. I am not referring simply to a tiger's claws, teeth and muscles, or a heron harpooning a fish with its beak. There is beauty in the unseen implements of death as well. Conotoxins are some of the smoothest weapons around. They are short peptides. Nothing more than a few dozen amino acids linked together, but a single sting from a cone snail, a single shot of those conotoxins can deaden all feeling, block all pain, paralyze all voluntary muscles, cause blindness, stop the heart from beating, stop the lungs from breathing. Killing it's victim once isn't enough. Cone snails manage to do it in a myriad of ways with one blow. The beauty of the conotoxins is that they are easy to make, there are many of them, and they have very specific activities so that they can also function as drugs. They can anesthetize a patient, relax muscles, and possibly even help with Alzheimer's, Parkinson's and epilepsy.

The cone snails aren't the only ones who have cornered this market, bacteria have similar methods. When they run out of food, they start secreting all kinds of toxic chemicals that can shut down the ribosome, or the manufacturing of the cell wall in other bacteria, and also digestive enzymes so that after killing their neighbors by shutting down their most basic functions, they can clean up the mess by eating them. That is where we get antibiotics from. We really don't invent most of the drugs we use. We simply find a fellow life form that makes something deadly and figure out how to collect or duplicate it. Who knows what organisms there are left to find? And in every place where we find life, we will also find the equipment for death, which we can beautifully exploit in an effort to preserve ourselves.

Work and Play

2011-09-25T14:49:00.000-07:00

I am busy these days, with good things and exciting things. Many (but not all) are written things. I keep getting invited to write book chapters about antibiotic resistance. At first i wasn't sure whether I should accept those invitations because I wasn't sure what to say. But then I realized that there is a lot I have to say and that if people want to hear my two cents on the topic, I will give them just that. So I have a lot of writing to do and I am smooshing the book chapters in between writing grant applications. That said, it is all fairly enjoyable writing, because I am learning so much. I am biting the bullet and learning about aspects of antibiotic resistance that have been opaque to me because of strange vocabularies and cellular mechanisms I never learned about. I sort of feel that I keep earning my biology degrees over and over again, or that I didn't really deserve them in the first place.

Barry and Sue Hall are going to pay me a visit at the beginning of October and we will have the first ever Bellingham Research Institute bioinformatics retreat up at Yosemite. There is internet, and nearly no phone reception, so it is a perfect location. Also, the Taft Point Fissures are there and no matter how many times I go to see them I will never grow tired of them. (Yes, I chose the location.) There is no way of showing in pictures how terrifying it is to look over the edge, or how beautiful it is to see Half Dome at eye level on the hike out, but here is an attempt.

Sadly, in my business, I will miss the first ever Barlow "Shoot 'N Q". After thirty years of living in a rural locale, my family is attempting to go native or something, by grilling meat while shooting guns off the deck at targets. They gave the shooting part a practice run. Considering that most people in my family have never shot a gun before, and that my dad is so opposed to killing anything he never went hunting (not to mention he that taught us to catch insects in bottles and let them go outside), this is a strange social event for my family to host, but I suspect it will be a lot of fun. As a makeup for my absence, I have proposed a biathlon for Christmas. It might be a good idea though to get some experience with a rifle before hitting the course.

Finally, there is a poem my sister Laura (shown above in hippie dress while shooting a gun as a display of political independence) had me read that I enjoyed and keep enjoying. It is about the inability to repay the goodnesses given to us. There are many people I can never repay. I am a lucky girl to have so many.

"The Lanyard"

The other day as I was ricocheting slowly

off the pale blue walls of this room,

bouncing from typewriter to piano,

from bookshelf to an envelope lying on the floor,

I found myself in the L section of the dictionary

where my eyes fell upon the word lanyard.

No cookie nibbled by a French novelist

could send one more suddenly into the past —

a past where I sat at a workbench at a camp

by a deep Adirondack lake

learning how to braid thin plastic strips

into a lanyard, a gift for my mother.

I had never seen anyone use a lanyard

or wear one, if that’s what you did with them,

but that did not keep me from crossing

strand over strand again and again

until I had made a boxy

red and white lanyard for my mother.

She gave me life and milk from her breasts,

and I gave her a lanyard.

She nursed me in many a sickroom,

lifted teaspoons of medicine to my lips,

set cold face-cloths on my forehead,

and then led me out into the airy light

and taught me to walk and swim,

and I, in turn, presented her with a lanyard.

Here are thousands of meals, she said,

and here is clothing and a good education.

And here is your lanyard, I replied,

which I made with a little help from a counselor.

Here is a breathing body and a beating heart,

strong legs, bones and teeth,

and two clear eyes to read the world, she whispered,

and here, I said, is the lanyard I made at camp.

And here, I wish to say to her now,

is a smaller gift—not the archaic truth

that you can never repay your mother,

but the rueful admission that when she took

the two-tone lanyard from my hands,

I was as sure as a boy could be

that this useless, worthless thing I wove

out of boredom would be enough to make us even.

-Billy Collins

This is neat!

2011-09-19T18:48:00.000-07:00

Fitness Competitions

2011-09-19T12:56:00.000-07:00

The good thing about being a scientist is that it is possible to obtain intellectual stimulation from personal predicaments. For example, at the School of Public Health Christmas parties I used to attend, which were always held at a cheap Chinese buffet in one of the peepshow and strip-club districts of Atlanta- worn-out carpet, dirty vinyl booths, and very greasy food- we would amuse ourselves by guessing which foods were the most likely to result in what kind of food poisoning, and discretely warning each other away from them. In the actual event that someone got food poisoning, it was even better because then we could try to work up the case and figure out when and which dish and what pathogen. Such fun!

Lately, I have been using similar powers of abstraction to find amusement in evolutionary competitions which have been taking place. In cases of personal evolutionary competitions, I usually view the whole situation as one of the "Sim" games. But instead of Sim-city or Sim-ant, I am a human stuck in the games "Sim Moth" and "Sim Bermuda Grass" (except they aren't "sim", they are real) . While I was away this summer, the competition invaded and got ahead, way ahead. The moths probably rode in on the brown rice, which I am willing to let them have (at the landfill), but after conceding defeat with quinoa, basmati rice, corn flour, granola, oats, cereal, dates, and any other food kept in ziplock or tupperware (don't ask me how they got through double sealed ziplock bags, but those commercials lie) I am ready to become the victor. I certainly hope I can out compete a few moths. My pride is on the line. And honestly, there isn't much left for them to take. And yet they keep emerging. I don't know from where. I am about ready to take drastic measures and bomb my house with insecticide. Perhaps I will go see The Help while I do. The book was great.

(The bermuda grass story is the same except it took the vegetable garden, and I am contemplating round-up.)

The things we need

2011-09-14T11:01:00.000-07:00

I have several collaborators. They are good scientists and good people and good to me. This makes "How antibiotic resistance evolves" a good field to work in. Overall, we are a friendly and open bunch of people who mostly just want to keep people alive and with all limbs attached, organs intact, and without carbuncles covering them.

There are not many of us who really study "How antibiotic resistance evolves", (which may be a part of why we value each other). There are many scientists who believe that they do study this problem, but they don't. Perhaps they believe, as some have told me "Evolution is everyone's favorite hobby." Perhaps it is.

When I think of that, I am reminded of the following excerpt of an NPR interview with poet Billy Collins:

Mr. COLLINS: ....... There's a lot of--the misconception is that you don't need to know anything to write poetry. I mean, one of the things you get when you say you're a poet is, `Oh, you're a poet? Really? Well, that's interesting because our daughter, Tiffany--she's 11--she writes poetry.'

(Soundbite of laughter)

Mr. COLLINS: And my revenge fantasy is that I ask this guy what he does, and he says, `Well, I'm an investment banker.' And I say, `Really? Because our son Timmy was playing with some change on the floor the other day. Such an interesting connection.'

Actually, there is a lot one must know to be an evolutionary biologist. Reading Origin of Species is actually not the path by which one becomes an evolutionary biologist. Nor is choosing sides in the Scopes Monkey trial. Nor is "believing in evolution".

There is a lot of highly disciplined training that is necessary, which usually includes math, theory, logic, inference, history, general literacy about the work of others and advances in the field, computer methods, laboratory methods, writing and oral presentation skills, and a blend of creativity and good sense.

To be able to really study antibiotic resistance in a useful way that can actually help people requires some sort of clinical training on top of that. There are not many of us who have completed all of that. Most of us who have are relatively young people who went to school for a very long time and have just arrived on the scene in the past decade with some sacks of tools and ideas about how to get in the way of evolving antibiotic resistance.

We are optimistic realists, but we have our work cut out for us for two reasons:

1.) We know nearly nothing about the evolution of antibiotic resistance beyond that it does evolve, in the most general sense of the word possible.

2.) (The more difficult problem) There are over 120,000 scholarly articles about antibiotic resistance, and so it is really hard to convince people that we know nearly nothing about how it evolves.

Sure, we know mechanisms of resistance, and when resistance first appeared, and the frequencies of resistant bacteria in countless hospitals, but how it evolves, and more importantly, how to stop it from evolving, we know nothing -- nada, zip, zilch. But there are people who think they do, and it is hard to convince them that they don't.

The dogma right now is that we have overused antibiotics, and so bacteria have evolved resistance. Therefore, using fewer antibiotics should solve the problem. But this explanation is waaaay too simple and the solution simply incorrect.

The solution to antibiotic resistance (and I am quite certain there is one) is much more complex. Bacteria are not as simple as a lightbulb connected to a dimmer switch, where as they are given more antibiotics, they become more resistant and when the are given fewer antibiotics, they become less resistant.

They are more like electronic components connected through circuits in a computer performing complex functions. Antibiotics are not the power driving the circuits, they are just keyboard commands. There is an awfully lot that goes on inside the bacteria and within there communities that occurs independently of the presence or absence of antibiotics, much like the internal processor of a computer. The keyboard commands (or antibiotics) merely feed into that process and alter or direct it somewhat. Rather than chips and diodes, bacteria have horizontal transfer, homologous recombination, fitness trade-offs, physiological limits, genetic potential, and genetic constraints. Understanding how these mechanisms interact and respond to the presence of antibiotics is what evolutionary biologists are trained to do.

And there are things that we need to be able to do this.

1. We need genetic data from resistant and susceptible bacteria.

2. We need phenotypic data from resistant and susceptible bacteria.

3. We need spatio-temporal data to understand the environment that bacteria exist in.

Evolutionary biology has some pretty powerful methods for inferring what is going on from these sorts of data, and with them , I am convinced we could learn what is really going on with bacteria.

Having these three pieces of data for a lot of bacteria would enable us to understand how resistance evolves, and how to throw in inputs that will essentially "crash" the system, or cause bacteria to lose resistance to some antibiotics.

Unfortunately, what funding agencies think we need are more antibiotics. But that is a bandaid solution. New antibiotics are more difficult to find now than they were back in the 1940's or even the 1980's. Even if we find some new ones that are good, I suspect that we might get 10 years out of them. Maybe 20 years if we are lucky...

Unless we find ways to manipulate and inhibit how resistance evolves.

To do that, we need the three types of data outlined above.

******************************************************************************

Dear funding agencies,

Please re-evaluate your priorities for addressing the problem of antibiotic resistance. Unless you do, you will waste a lot of money, a lot of time, and still have no lasting solutions.

Best wishes,

Miriam

If my brother learned code to patch in his games when my dad switched over to ubuntu, then surely I can succeed.

2011-09-13T19:18:00.000-07:00

I have decided to REALLY learn to write computer code this time. Perhaps I will succeed this time. There are reasons that I might succeed:

1. I am trying "R" instead of Perl or C or C++.

2. I am better now at turning chaos into order.

3. I have learned to keep rhythm better.

4. I used to think I couldn't learn Spanish and I am learning Spanish anyway.

5. I type faster than I used to.

6. I only read off of an ipad anymore?

7. ..........

............

If this doesn't work, perhaps I will try some neurofeedback.

Wish me luck.

Grape season

2011-09-10T22:06:00.000-07:00

Two missionaries picking grapes.

Harvesting grapes is dusty, juicy, messy work, but it was the perfect way to end a week that seemed like it would never end. Throughout this week, I have been astounded by how much very real distress results from the virtual reality of cyber-space. And so it was reaffirming to do the hard physical labor of picking grapes and laying them out on trays to turn into raisins in the sun. I worked along side friends in a welfare vineyard, which is pruned, harvested and maintained by volunteers. The products of our efforts feed the poor, and when there is excess crop, the extra raisins are sold to Sun-maid and the money from that is also used to assist the poor.

Everything about that work is really real. Waking up at an early hour to have some time before the day heats up, and when the day does heat up, the sun beating down and caking sweat, dust, and grape juice on the arms of the workers. The dust billows around the ankles and knees of any and everyone who moves. And in the back of the minds of everyone there, the purpose behind our being there: Hungry children.

Dentists, attorneys, school bus drivers, college professors, electricians, manual laborers, children and retirees work side by side and discuss everything including fruitflies and spiders, politics and the economy, personal successes and sorrows, gentle teasing and jokes. Personalities sometimes clash as one person attempts to instruct another on the best ways of doing things, but the purpose of it all ultimately keeps the peace. And everything about it is real. There are people who lack food; this is where food comes from; at the level of the physical need, we are all equal.

What else is real is that the people who work there have hope, for themselves and for others. There is a sense that all problems are solvable. We produce raisins, and at other farms that are run the same way, there are pears, peaches, oranges, wheat, corn, etc. Where the land is not so good for farming, volunteers make quilts, bundle clothing, wheelchairs, and eyeglasses to ship to developing nations. It is possible to make a difference for good, and in small and gentle ways we are doing that.

(Moral?) Dilemma

2011-08-28T15:50:00.000-07:00

I don't drink. Probably mostly because I am Mormon, but if I wasn't I still wouldn't because alcoholism runs in my family and I take some pride in being in the functional demographic at family reunions, so maybe it is really mostly because I don't want to be an alcoholic.

Mostly it works for me to not drink in professional situations. (The issue almost never comes up in social settings because my friends know me.) Sometimes someone will insist. (Usually a guy who relies on alcohol to get girls into bed, or a senior scientist who thinks I should imitate her.) Scientists rarely respect my religion, but if not that, then they respect the undesirable response my genetic make-up would likely cause me to have to the environmental stimulus of alcohol. (After all, scientists figured out that genetics can predispose people to alcoholism, and we like to feel that our work is important.) If that doesn't convince them, then they must defer to my stubbornness on the matter. So I have no actual experience with drinking even though I have been around quite a lot of drinking and drunk people, and generally I have fun as the only sober person, because everyone thinks I am funny, even when I tell really lame jokes. It is kind of fun to see how good of a response I can get for a really lame joke. When people are getting too drunk to respond any more, well, then it is time to go home.

So here is the dilemma, I need to teach certain aspects of professionalism to a cohort of graduate students, and I am not sure what to say about drinking. I remember Barry Hall trying to give me advice on professional behavior at conferences, and he was telling me not to bring strange men back to my room, and something about drinking and I started laughing and told him not to worry. I now wish I had listened, so I would know what to say.

So if you have read this and have some sort of wise advice about what to tell a bunch of inexperienced graduate students about drinking, or not drinking in professional settings without making fools of themselves, then please share it with me. I will be most grateful.

I am back and fun tonal

2011-08-26T09:36:00.000-07:00

I am a wimp when it comes to jetlag at home. Going east hardly phases me, but coming back sort of smashes me over the head hard. I sent Kristina Crona an email to let her know I was home and functional again. It was so full of typos she gave me a couple of days before responding.

There is work waiting for me. Most of it is writing grants and manuscripts, and organizing seminars this semester. Before returning to all of that though, I want to jot down a few realizations.

It sort of started in Spain. There is this combination of highly developed conversational etiquette combined with a work day that starts at 10:00, breaks at 1:00 for lunch, resumes at 3:00 and then ends at 6:00 9the building closes and they kick you out), that got me thinking about America, and why we don't do the same things here. There is an acknowledgement of life, emotions, comfort and humanness in Spain that just isn't part of American culture at all. And I understood why Americans are considered rude by so many.

As I sorted that out, I had a simultaneous realization that America was founded by destitute immigrants, who for whatever reason, had forsaken their homes and had come. Most were probably considered rude and unmannered as well. Their struggles for the means to survive echo through modern American culture.

I see the mark they left on America in the long hours so many Americans work, the direct attention and priority given to business, the opportunity for anyone to obtain higher education at any point in life, the priority given to independence, the absence of graphic design in most daily articles, and in our money. It strikes me that "In God we trust" is as much a statement of defiance to the privileged and powerful as it is a declaration of faith.

When I contrast these aspects of American culture with current trends in American politics, it strikes me how un-American our political movements really are. From the left, there is a strong push towards socialism, and from the right a strong push towards anti-intellectualism. Both sides are pushing against the idea that any person may become whatever they will through hard work and education. There are simultaneous pushes for financial incentives for unemployed illegal immigrants and to expel productive and hardworking immigrants. There are one dollar coins that lack the words meant to defy earthly powers.

After thinking through all of these things, I found in Switzerland a major political movement to stop all immigration.

There are signs protesting immigration everywhere, and this is the most benign (posted with reluctance).

I know that there are problems with immigration in America, and I don't claim to have solutions. I suspect that with every major wave of immigrants, there have been difficulties to overcome. As I consider them however, I find I am a lot happier with the problems of immigration, than the alternative of having no immigration. And I hope that the aspirations and efforts of immigrants help maintain the American-ness of America.

A collection of important details that may or may not be connected

2011-08-16T15:29:00.000-07:00

My course on public health is now complete. I am tired. I lectured a lot of hours and prepared ever so many more. It went over well I think. The minister of health for the Valencian region came the last day and took pictures with us which have been appearing in newspapers. It is kind of exciting. I had mentioned that I might like to go on sabbatical there and they announced that I would be during a speech for the minister, so I guess I really will. I will probably do so in 2013, if all goes well. I like the researchers there. They like me, and we work well together. They have good data. I have ideas about what to do with their data. There is a lot of potential for excellent collaboration.

Aside from that, I have learned so much from Spain that it is hard to know where to begin, so I'll start with Picasso, because he is important. It is not so much what he chose to paint that astounds me, but how he could convey the most important aspects of a person with five or six brushstrokes. He could reduce all the elements and complexity of a person to a few critical defining elements, and a viewer of his paintings can get the sense of knowing a person in a painting many years later. I envy his gift. I try in my science to take the same approach, but somehow I lack the power he had in conveying the few critical elements, and so I waste time dallying with trivialities. I am going to think about Picasso every time I design experiments or write about them. It will do me a great deal of good I think.

Joan Miro affected me differently. As I starred at the abstractions that visually summarized his life, attitudes and ideals, I saw a man obsessed with groping breasts, clearly a bad lover, at least two girlfriends who killed themselves, and who had a firm grasp of the disconnect between potential and reality. In a few brushstrokes he defined himself, and I found myself trying to identify the five or six elements of my life that define me. I am still thinking about that. I also came to the decision that there are a lot of bad men in the world. They may have potential for being good men and they may have good in them, but I think many of them are overall just bad. Seeing things from that perspective, it becomes easier to recognize good men. They don't generally get enough credit for being good, but they are so important.

I have also learned that I really must learn Spanish. I need it far too often to ignore it any longer. I am also learning Catalan. I know the words for chocolate and churro, so that seems like a good start.

I am in Switzerland now, visiting family. I am happy, and sleepy and I feel good and well loved, both by family and by friends. My eyelids are slowly closing more and more, so it's time to cal it a night.
Good night.

Spain!

2011-08-03T07:07:00.000-07:00

I am in Spain, at the Generalitat Valenciana Centro Superior de Investigatión en Saludo Publica. I am here with my lab group and the next-lab-neighbor Maria Avila. Jetlag has been overcome. We have made friends with the locals. They love us and want us to be facebook friends and go to beach music-fests and such. I have picked up some female-centric graphic design souvenirs (paper place-mats, utensil holders, etc.). I have a favorite café and a crush on the hardware store guy who made key copies for me. I successfully found, purchased, and installed (with Maria's help) a toilet seat in the apartment we are renting. I have tasted, enjoyed, and grown tired of Jamon Iberico (Ham made from free-range pigs fed with acorns or something ). I prefer the mariscos. Octopus is my favorite.

As for the work, we are learning about bioinformatics and sequencing this week. Next week, I will do the teaching. It will be some crazy sort of walk through all of the science that I think is important and therefore think about and work on. Hopefully, it will make sense. I have never been given so much creative liberty in such a lengthy presentation before. Unlike my regular classes, I am not constrained by a textbook, or medical school requirements. Unlike international research conferences, the two or three people who most love trying to refute my data are absent. I will try to keep things reigned in, but without their presence I may appreciably branch away from scientific canon. A part of me says that is what I am here for, and the other part of me warns caution. I shall see which one wins out in the end.

Home.

2011-07-25T10:58:00.000-07:00

I am home, which means American Fork,Ut.
(This photo was taken by my mom from her deck.)

I finished a wonderful week of science and other activities, and have now come for a wedding.

I drove through the high desert for 13 hours with two little girls to get here.

Their parents will come Tuesday, which is when Tom will be able to get leave from the Navy.

Yesterday, Mattie handed me a fistful of paper scraps for me to throw away and when I protested, she informed me that until then I am basically like her parent for now and that parents take trash from children when there is no trash can in sight.

There are cousins here for them to play with since Marie and her children have also come. Last night they prepared and performed a musical performance for all of us that included whistle blowing, a glockenspiel, clackers, drumming, and hula hooping. (There are videos which I am certain are not as cute to non-relatives as to me, so I won't post them.) We all laughed and cheered.

After that I went to Laura's final undergraduate art show. It is filling the main atrium of the Harris Fine Arts Center. It is receiving a large positive response. It is about grief and features so much clutter that has accumulated through the years.

At the head of the bed are piles of books. Four of them have their spines turned away so their titles can't be seen. They are the ones I donated to the exhibit. After Marie had a miscarriage a few years ago, I went to visit her as soon as I was able. She told me to read Twilight before I came so I could discuss it with her. I had been resistant to reading vampire romance novels, but for a grieving and recovering sister, I would read just about anything. I read. We discussed. We have been reading and discussing books ever since. Around the time we read and discussed Good Omens, she discovered we are best friends. I am so happy that Laura found a way of including my Twilight books in the exhibit.

Sleeping Scientists

2011-07-18T21:57:00.000-07:00

There are two little girls falling asleep in my back porch room. I just calmed them down from their mutual recollection of some South American zombie story that their uncle felt compelled to share with them. (Please note Ethan, that if you ever tell them scary stories again before they come to stay with me, I will give you something to be really frightened of.) They have come to do science with me. Emma, the oldest is nine, and Mattie is seven. They are both brilliant and capable and I am continuously surprised by how much they understand. (I had pretty high expectations, or I wouldn't have invited them to work with me.)

So far, we have pumped agar into plates using a peristaltic pump, and we have streaked bacteria on the plates we made. Anna, my lab manager, taught them about the clonal division of bacteria, and showed them how to plate cells after a transformation. Tomorrow we will inoculate cultures.

Both girls are excellent in the lab in their own unique ways.
Mattie decorated my bleach bottle with a diagram of dividing bacteria, so that no one will steal my bottles of bleach any more. She is always on my heels and tries to do everything I do, asks about every piece of equipment, and concentrates hard.

Emma is more reserved. She renamed agar "ogre" because it smells the way she imagines an ogre smelling. She avoids touching things because she doesn't want to wash her hands as often as I make them. Her curiosity always wins out though, and she pushes to take her turn doing everything. She asks her own questions as well. She has good hands, and did a beautiful job streaking bacteria on a plate, and I suspect she will become very good.

My friends have all made generous offers to me to help keep the girls entertained in the off hours, and we have been busy. They have the general impression that Merced is some sort of paradise, and with them here it is. We went to the California Academy of Sciences Museum and Ghirardelli Square for ice cream. A couple days later, we went to Hornitos, a ghost town featuring the original Ghirardelli factory. We peaked inside the windows of homes abandoned back in the 1940's or 50's. I have no idea why old stoves and dilapidated sofas are so cool in an abandoned home, but they are. That night we were invited by Cambria Brown to an art hop that featured face painting, foot painting and street painting for children. Sunday was with the Shaw family who are back to Merced visiting because Professor Glen Shaw has a summer job with the forestry service studying water flow or something like that. Their children ran with my nieces for hours. My house survived thanks to Ana Shaw, who knows when enough is enough. Today we cleaned out kayaks with Lynda Dyas for our kayaking trip tomorrow and then swam in a borrowed pool whose owners are away, and we picked ripe peaches from their peach tree.

I will post pictures later. I finally broke down and replaced my stolen camera because I need some pictures of these two. The battery for it is charging now.

Thinking about Faulkner

2011-07-11T10:41:00.000-07:00

I have started listening to Faulkner on audiobook. I haven't had much time for leisure reading and when I have tried to read, I have found myself getting bored and wanting more of a challenge.
It isn't really a reflection of the literary works so much as my state of mind right now.

I am grappling with bioinformatics approaches to defining everything microbial. That project combines epidemiology, genomics and clinical micro. The science isn't exactly hard, it is just a new perspective that seems to make a lot of sense right now and that has hardly been touched upon before. Having established a bit of firm conceptual ground from which to work, endless possibilities seem available. Creative fireworks are going off all of the time with me and my collaborators. It is science as it ought to be. Satisfying, productive, and so much fun. Hopefully it will be useful in the end.

My other intellectual pursuit, which I don't blog about very much at all, is studying Biblical imagery, and I am grappling with Isaiah. I understand a bit, do not understand quite a bit, and have figured out a few things I did not understand before, so that is pretty satisfying too.

And a final mental exercise put into practice is organizing and caring for my house. It is a way of dealing with the things I can't control or fix. For example, I couldn't find my box of X-Acto knives last night and I realized that it was taken when my home was robbed. That is something out of my control. However, where I keep the things I do have is something I can control. Somehow having a well-organized home makes me feel empowered. I am not OCD. Children are still welcome. But I love the mental challenge of figuring out how to coordinate the motions of my domestic duties with the physical objects of my house.

With all of this going on in my head, how could any old average book hope to hold my attention? (typed with a little sarcastic smirk on my face.) So I went for some Faulkner. Also and mostly, Marie has been reading As I Lay Dying, and we try to coordinate our reading so we can discuss the books. I still have a long way to go. The dead woman has barely been put in her coffin and so far from only three different perspectives. I have several hours left of listening. I love it so far though. It reminds me of so many things I love. Like cathedrals in France which are magnificent structures of Christian faith and yet pagan symbols and astrological signs were included in the workmanship for good measure by the humans who built them. And sometimes there is the smell of urine from the humans who visit them more recently. They are simultaneously so grand and so base.

The other thing it reminds me of is driving through rural Mississippi. A turkey jumping out of a tree right in front of my moving car, rain storms where so much water fell through the air that I sometimes questioned whether I would drown if I continued to breathe normally as I went outside, and mostly of getting lost. I called my Uncle Allen when that happened, sure that I was lost beyond hope. I was in a place where road signs didn't exist, there were no structures, there was nothing that stood out as a landmark. He just asked me to start describing things to him. The shapes of the hay bales. Whether there was a rock on the right side of the road; not real big, but big enough you could see it and it wasn't going any where. The fence. The color of the dirt. From those details, he knew exactly where I was and guided me exactly to his house. I couldn't even fathom remembering those details.

And as I listen to a reading of Faulkner's work, which roams through the thoughts of so many so different people, I am in a state of awe. They are all so real and believable. The details are a perfect recall of real humans. The text, flawless in construction and the characters so tragically flawed. It occupies my consciousness and my thoughts about science, imagery, and order, all struggle to compete with Faulkner.

A quick ammendment

2011-07-07T23:46:00.000-07:00

Béla Fleck's "Poindexter" is an irresistibly adorable love song.

Language training

2011-07-07T12:21:00.000-07:00

I am amazed by how many languages are nested within what we call "English" and I don't mean languages like Ebonics, pig-latin, or gang writing. Using good and proper English grammar, there are still countless languages. I tell my genetics students that a bachelor's degree is basically awarded for learning to speak the language of whatever major they are following and that they need a good dictionary to help then through. Many students often smirk at me and word has come back to me that they think I am condescending. They take me seriously though after coming to my office hours, unable to understand their text book, and then spending an hour or so with me simply looking up words in the dictionary. They always leave understanding biology much better.

I give myself a similar mental speech when I find myself particularly frustrated with literature from some new field that I am reading and then slow down and learn what the medical terms or population genetics terms that I am reading mean. I feel like a serious chunk of the past year has been spent learning to speak new languages. The biologically and medically related languages have gone pretty well. For example, I think I have a decent grasp of epistasis in all of its variations. I thought I understood before; it is simply non-additive genetic interactions. But there are so many ways of achieving epistasis and so many variations on it that a mini-language has been formed to describe them all. It is a language in which I am fairly certain no love song will ever be written (and I think that love songs, somewhat annoyingly, can be written in almost any language) so I will not go on any more about it since it probably lacks universal appeal.

Writing up math papers has been more challenging. Although English is definitely involved in writing about Math, Math exists at the fringes of verbal language. (That said, I am entirely confident that love songs could be written in Math and performed fairly capably by They Might be Giants. However, I am also fairly certain that most of their fan base wouldn't understand them so they probably wouldn't be great money makers.) As Kristina speaks Math and I speak Biology, finding the right words to communicate in can be really quite difficult. She speaks biology with such a strong mathematical accent that sometimes I have a hard time understanding. I speak math with such limited abilities that it probably sounds like clicks and whistles. We often end up communicating with pictograms and it is effective enough to get good work done. The real trouble is though that Math is such a specialized area of language that normal word processors aren't great environments for writing about it. Krisitina likes working in scripting environments where equations are easily added. I can't say that I love writing in Microsoft Word, but it's what I know, so it is what I write in usually. We have reached a compromise of writing the initial draft in her scripting language, doing all of the editing in Google Docs, and then converting the final draft to Word for the sake of the publishers. (It seems to be working for both of us, so I am not going to mess with it unless we find something better.)

Thankfully, the more exposure we get to each others languages, the more fluent we become. Kristina is taking off in speaking biology like a biologist and I am getting to the point where I understand most of what is being said in Math. The written versions of all of our work are becoming much smoother and I think they will be good enough to get published pretty soon.

*

Academic Doping

2011-07-06T14:10:00.000-07:00

In my somewhat ancient past when I was a pre-med and planning to become a neurosurgeon, the graduate students I worked with loved teasing me. They saw me more clearly than I did and knew I would end up a scientist, but I was awfully stubborn about giving up on my plan. If I hadn't found and fallen in love with evolutionary biology, I am not sure I would have. They used to tease me about cheating, tearing down answer keys and sabotaging other students because that was what pre-meds did. They actually knew better, which made them comfortable in their teasing. I was at the tail end of Gen-X, almost a millenial, and the culture of premeds was changing. Of course we pre-meds competed with each other, but it was more by subtly showing each other our test scores than by anything else. We let the corner of the exam with the grade on it stick out of a stack of papers or left an exam on top of a book at a table. We all knew where we ranked and we fought hard to rise higher. But we didn't do it by harming one another. That was suicide. There were a couple of kids who tried that stuff and they were ostracized. Most of us studied together and tutored each other. If you could teach something, you knew it. We competed to be the one teaching the group.

From everything I see of students today, that culture continues. The students at UC Merced are sweet. They help each other as much as they can. There is another aspect of pre-med/ med school/ residency culture that has recently (ish) emerged. It is the use of performance enhancing drugs. It turns out that students on A.D.D. drugs can learn more, study longer, remember better than without the drugs. So a lot of students are finding semi-legitimate and illegitimate ways of getting their hands on drugs meant for sufferers of A.D.D.

This one worries me a bit. The drugs for A.D.D. are all relatives of amphetamine. So is crystal meth.

I have spent significant amounts of time with a crystal meth junkie. I used to collect her son and take him with me to other places besides his home. He would always say "I'm comin' with you" and never asked where we were going unless the drive got long. His mom's driveway was booby trapped with boards that had several long nails poking through them and hidden under autumn leaves. I was so happy she told me that before I walked or drove down it.

I also know a young boy who suffers from A.D.D. and has shown several similar symptoms of paranoia and depression as a response to his medication. Thankfully he was under close supervision of loving parents and his meds got readjusted so he is fine.

I also sometimes have students who come to my office a little paranoid about their grades and worried that I choose favorites and discriminate, which is ridiculous because my grading is transparently cut and dry, and if anything excessively merciful.

And now I am beginning to wonder whether the paranoid students have something in common with the other excessively paranoid people I have known... Namely amphetamine.

The olympics have tests for doping and many competitive sports require regular doping tests. I would love it if we could test for doping in colleges. Although if that ever happens I do not want to be the one collecting the cups of urine.

Gravity

2011-07-05T03:08:00.000-07:00

My first memory that is anything more than the sound of falling rain is of a water lily floating in a pond. Marie wanted to know how it floated and as my mom reached across the water, nearly falling in to get it and show her, my mind was furiously at work. I was jealous. There was the general jealousy of Marie's ability to walk and talk as I sat there, strapped into the seat my mom used to carry me around in. But the real cause was that Marie had thought to ask what held the water lily up and I hadn't even wondered. I had simply been appreciating its beauty. In a desperate attempt to feel as clever as my older sister I tried to figure out how the water lily floated before my mom could lift it up. I hastily imagined bubbles formed by delicate membranes, and then realizing how easily those could be broken, I imagined a coarse and spongy tissue that was less pretty, but buoyant and more durable. It seemed so likely to be the correct solution for how to make a lily pad float, that I was shocked and disappointed when my mom, after almost falling in, announced that there was a stem holding the lily pad up.

I am sometimes surprised by how little things have changed some 33 years later. Marie is still the clever one, finding wonder in strange and hidden places, and I am still the one who tries to figure out how to make things float. I cannot tell most of the stories of the things that I have tried to make float. They belong more to other people than to myself. The few examples that are solely mine center around updating a sixty-some-odd-year old house, and publishing zero budget scientific studies. They are somewhat boring stories, so mercifully, I don't usually tell those either.

I usually do pretty well at making things float. Marie once described me as a person who could suspend the Eiffel tower upside down upon the top of the Statue of Liberty with a single tube of super glue, and a single role of duct tape. I strongly suspect in that situation though, things would eventually come crashing down. And sometimes in real life situations things come crashing down as well. I think that right now is the time when I am most scared of that. I remember a math teacher who said that the peak of uncertainty is at the end of adolescence, but I feel like that for me, the peak of uncertainty is now, delayed by 15 years.

So many critical moments in my life have been delayed. Like when John, one of my best friends from kindergarten through college, got killed in an auto accident. A year and a half later as I was walking down a wooded path, near the Genesee River in almost the exact location where I had seen fireflies for the first time, I started crying and it was finally for John. I talked to Matt Meyer about that after another friend passed away. Matt said that it was just that I was trying to survive and when the pressure let up a bit, I would finally deal with those emotions. The little parts of me screaming in fear and sorrow would out from quarantine to be tended to. He was right.

It is strange to experience those sorts of delays. Everything for me used to seem accelerated. College in three years, grad school in three years. Then, as one of the very few scientists qualified to discuss evolution and clinical microbiology and the health problems emerging from the combination of those two fields, to be the youngest by 30 years in rooms of important people discussing better ways of saving lives. Dealing with loss on paper is easier than dealing with the deeply traumatic non-theoretical variety. It goes a lot more quickly.

It only takes an out of control semi on a freeway, or an out of control cell growing in a pancreas to send life into free fall. And in those delayed moments, when I finally catch up with no longer relevant events I sense how very futile it is to try to keep what is dear to me afloat. A friend of my mom's once said that I was the glue holding things together. Several years later, in so many ways, I know that I am not.

Around the time that I really realized that free falling is an unavoidable part of life, I also realized that there is gravity. No one understands what causes gravity, only its effects on falling objects. While it can sometimes cause glasses to break, knees to be scraped, and heads to be bumped, it also shapes the free falls of planets and stars into the orbits that form solar systems and galaxies. It keeps things floating in a much more robust way than I could have ever imagined.

And in my own world, my family is the gravity that holds my orbit. So immediately after submitting the large number of documents required for tenure review, I did my best to suppress nausea, packed my car and drove to Marie's house to see my family. The occasion was the eighth birthday and baptism of her oldest daughter Katie and a great party celebrating so many things. It was wonderful and busy and ultimately entailed me going down a slip and slide on my knees in a dress. It was more fun than I thought it would be and totally worth it. (Though there will always be a bathing suit stashed somewhere in my car from now on).

Marie and I also celebrated our own birthdays late and in a fun way. Laura brought us a present she ordered ages ago, but that took ages to come. She gave us BFF necklaces that are in the form of base paired nucleotides. I got guanine (G) and Marie got cytosine (C). Laura chose those with the help of her biologist boyfriend, Andreas, because they form three hydrogen bonds and are the most stable nucleotide pair. She said she chose them with Marie's permission because they love having a scientist in the family. My orbit will always bring me around to such dear people and I have every hope that their orbits will bring them back around to me.

Truth through fiction

2011-06-30T13:04:00.000-07:00

After two weeks of barricading myself away to get a lot of writing done fast, I am almost done with the dreaded tenure materials (and my various other projects with similar deadlines). I have found that pajamas are probably the most effective clothing for completing heroic writing efforts, and I strongly suspect that they would be great for completing heroic amounts of lab work as well. (Don't worry concerned loved ones....I will not start going to work in pajamas....at least during normal hours. For 3:00 AM lab runs, all promises are off.)

The real key to writing about how great I am was talking to Barry. I put him in the place of Anubis (he is much friendlier) and he listened to everything, all of the criticisms I have received as well as my successes and assured me I have done just fine. And while he is undoubtedly biased in matters concerning me, I have always felt that made him push me harder rather than taking it easy on me. If he says I have proven myself, I'll believe him.

When I emerge from this isolationist approach at writing, which I long to do, it will be to do more writing, and some reading, thankfully.

My graduate student Christiane Goullart just finished up a massive study of adaptive landscapes that has taken five years. The computer programs necessary for analyzing her data are written and the analysis is almost done. Now we just have to explain to everyone why her work is so great. That will be fun and easy.

I am also working on a pile of math papers with Kristina Crona, who sadly, is seeking employment elsewhere. We have a lot to get done before she leaves.

And as for the reading, I need to learn as much as possible about every strain of E.coli that has ever had its genome sequenced for a new project that I can't talk about yet, but that I am excited about.

I have also been entertaining the idea of writing a bit of fiction. I have a story developing in my head about what would happen if scientists became the dominant political power in America. The way the story is going is really quite dark and I am discovering some interesting truths about my views of things. I find my greatest fear is no longer entropy, and instead is of scientists setting social policies based on their lab work. I also find that I regard high schools as being similar in many, many ways to prisons. And that when religion is linked to social status, it has the effect of creating gang-like social structures. I am now looking for humor in this fictitious setting, and unless I can find enough, I won't write the story.

I think that my studies of antibiotics are important for keeping modern medicine useful, and that scientific studies in general are critical for improving human health and technology. But I also think that there is more truth about what being human is in a good work of fiction than in the whole human genome sequence. However, believing in fiction is one thing, making it come off well is another.

Hero quest

2011-06-28T20:59:00.000-07:00

My lilly trees are all in bloom and sometimes I catch the faintest hint of their fragrance in the breeze that is blowing. I am sitting in my favorite spot beneath the lemon tree, which has a new crop of walnut sized green fruit growing in while the last remnants of the old crop are still hanging, ripe and yellow. It is my favorite spot because it always smells like lemons, but this evening, I mostly smell rain, blending sometimes sweetly with the lilies. I came outside to smell the lilies and breathe and rest from anxiety for a bit.

I am nervous. There is no doubt about that. I feel as though I am standing before Anubis, proffering some sheafs of paper and hoping to not be devoured. I have a serious problem with having so little control over the decision that will determine the course of my chosen career. I am not sure if that is good or bad.

In an effort to combat my nervousness, today I dressed in biker boots, black skirt, red top and an enormous belt buckle. I thought it looked comic book super-heroish and that maybe the clothes would help me see myself in some heroic light and therefore write about myself more persuasively. The result was that I got told I was hot a few times and checked out several more times. It turns out that there is nothing heroic about super hero clothes. They are mostly about sex appeal. I was basically hot (the other kind) and sweaty so I peeled off the boots and went for the silver pumps stashed in my file drawer instead. Mmmmm. Much better.

(A fair amount of productivity working on the tenure package occurred anyway.)

Tomorrow I think I'll wear sweat pants. If I feel a sudden burst of heroic inspiration, maybe I'll try to start a new trend in comic books.

Mysterious Universe

2011-06-26T19:12:00.000-07:00

I like working with bacteria. They are the foundation of life on the planet, (along with sunshine, I suppose). They do everything. They can solve nearly every problem, if properly persuaded. More than that though, I think that I can think like bacteria (not that they really think). I sort of grasp their raw struggle for survival....their deep commitment to obtaining food, their redundant gene sets that protect them from mutation, an arsenal of poisons for killing and eating other bacteria (I won't call it cannibalism...many of them are more distantly related than we are to plants and I never feel cannibalistic eating spinach or carrots), survival by cloning themselves, and a variety of random processes through which they add new DNA to their genomes and interact with their environment. They are simple, straight forward, and in their pure simplicity, they accomplish tremendous things. They decimate human populations more effectively than the most cruel dictators, they produce so many of the medicines that save human lives, they produce fuel and clean up oil spills, they decompose trees and provide nitrogen that makes plants grow. They are amazing, and I have learned enough to know how to ask them how they are going to do something, or what they will do next. I ask a direct question, I get a direct answer. There is sometimes, (rarely) a little teasing involved. And the answers almost always make sense.

I do not want to be a bacterium. I like being human, but sometimes I am envious of the straightforward approach that bacteria take. The ability to ask direct questions and get honest answers is really nice. There are such basic mysteries about humans that I would love to know the answers to, but it would be rude to ask, and I would probably not get an honest answer if I did.

For example:
Why do women take so long in bathroom stalls, especially when the lines are very long?
( I may be one step closer to discovering an answer after discovering Spanx.)

Why do men always want driving directions in terms of north and south rather than left and right?
And what is one supposed to say when a man asks whether he should go north or south on a road that runs east-west?

Why are purses considered the ultimate status symbol for women when attributes such as use of language and manners are much better predictors of where a person will end up in society?

What do men think about when they go into "the cave"?

As a scientist, I am deeply curious about all of these questions and sometimes the desire for answers nags at me a bit. It is sort of like that old TV ad where a boy asks an owl "How many licks does it take to get to the tootsie roll center of a tootsie-pop?"

I am glad there is science which gives me answerable questions to think about instead.

The "cure" for HIV

2011-06-17T08:07:00.000-07:00

Last December, there were reports of a man who had been cured of HIV through a stem-cell transplant (which is an up-to-date and slightly vague way of saying "bone marrow transplant"). Apparently the man was given bone marrow from an individual with an HIV resistance mutation. Much of the immune system is derived from bone marrow, and so the transplant from an HIV resistant individual to one with HIV resulted in the elimination of the virus.

There are problems with this cure though....finding bone marrow matches is difficult. Among non-related people, the chance of finding a match is ~1 in 20,000. Finding bone marrow matches with HIV resistant people is even more difficult, because the mutation is at a very low frequency in human population. About 1% of bone marrow matches among caucasians would be resistant to HIV. Which means the odds of finding an HIV resistant match are 1 in 2,000,000 for caucasians. For people of non-European descent, the odds are even lower because the HIV resistance mutation is at a much lower frequency.

Not even factoring in the high cost of bone marrow transplants, the improbability of finding HIV resistant bone marrow matches makes this "cure" impractical in the places where it is needed the most, such as Africa. However, there may be some practical uses for the discovery in Africa anyway. Over sushi the other night, Kristina (resident mathematical genius) and I were discussing transmission dynamics for HIV in an effort to come up with some realistic mathematical models for recombination in viral populations. Over the course of the discussion we came upon the topic of "hubs" for the disease, which are people who transmit HIV to more people than anyone else. In practice, they are most likely promiscuous men infected with a variety of sexually transmitted infections because the promiscuity increases the number of chances for infecting others, and being male and infected with lots of pathogens increase the probability of transmitting the disease with each contact.

Mathematical modeling shows that preventing transmission from "hubs" prevents transmission of HIV a lot, actually more than one would expect just by looking at raw estimates of contacts and transmission rates. I have no idea how many "hubs" there are in Africa, but it seems like doing everything possible to identify them and find HIV resistant bone marrow matches for them might be a way of turning a "cure" for HIV into an effective preventive strategy.

Finish line

2011-06-13T17:26:00.000-07:00

My house smells like plums, there are stickers in my feet, and the weather is perfect for skirts and sitting in the shade, which is what I am doing now while I take a break from preparing a course about genomics, epidemiology, and antibiotic resistance that I will spend a week in Valencia teaching.

I'm happy. The incubation period for tenure is over at the end of this month. For better or worse, I have done what I can and now I just have to tie up a couple of things, write them down on paper and then wait. There are senior faculty telling me that I am a shoe-in, and while that is comforting, it will just be nice to finish this part of my career. I will finally know whether or not I get to be an evolutionary biologist when I grow up. And if I make it, I will be able to think in terms of long term goals and career decisions, rather than producing as much as possible as quickly as possible. I will be able to pursue new ideas and directions with less fear and worry.

Perhaps I am simply in the eye of a hurricane, or perhaps the storm will finally pass, but for whatever reason, life is good right now, and I am enjoying that.

The hats I wear

2011-06-07T09:29:00.000-07:00

I get a lot of requests in my line of work. Health advice from family and blog readers....life and love advice from students....career advice from countless undergrads....and occasionally, I get more colorful requests.

Mostly I try to help and I am happy to. However, sometimes I am unable to help and those requests are actually the most fun. Here are some of the best:

-A letter asking me to isolate antibiotics from desert soil samples some good citizen was collecting.

-Several urgent phone calls from the county health department asking me to identify a snake who had bitten someone. (This one only became fun when I learned the snake was non-venomous and the patient was fine.)

-A phone call from Yosemite National Park Museum asking me to store a large historical specimen.

I still haven't found out what the historical specimen is....if it is a stuffed moose, I am not interested. A stuffed wooly mammoth, and I might be. I have no idea where I'd keep it, but I'd charge a nickel for everyone who wanted to see it.

Time travel

2011-06-05T14:49:00.000-07:00

I reached two important milestones this weekend which both indicate that it is time to return to blogging. The first was that I discovered my case of drill bits is missing, which made me feel furious..... nothing more, nothing less. The second is that I stepped on a nugget of broken safety glass which felt a bit uncomfortable....and I didn't feel like boarding up every window and turning my house into a barricade. I decided a couple of months ago that when I achieved those two goals, I would go back to blogging.

I don't really know where the drill-bits have gone or where the safety glass keeps coming from. The original source of the glass was the window of my back door, and after getting tracked through my house first by an unknown person, and then police and a detective and then by me, I don't seem to able to get rid of it all. Maybe there are some bits under the dryer that tumble out from time to time.

I have some random thoughts about burglary that I would like to share:
Home burglary has illustrated (yet again), that I am a nerd. In between being grateful that stray cats had not moved into my home during the week I was gone (in which the burglary occurred), I kept being grateful that I spend my money on education and travel rather than on stuff, because not that much was taken. I was most offended by the theft of my camping gear because it was the most expensive loss, but I felt most violated by the removal of my Dremel tool. It was funny that I could wade through underwear and bras tossed everywhere in my house with the police present and feel no shyness, but then a couple days later burst into tears and shut down when I found my Dremel was gone. Another funny thing was that I also felt an amount of scorn for the thief because they didn't even glance at my books. Not that I would ever be a thief, but if I was, I would probably go through the bookshelves. That said though, the funniest thing was that my scriptures were taken. I do not understand that at all.

The most fun thing about getting robbed is the extended version of a slumber party that happens afterwards. I have good friends who would have let me sleep at their houses indefinitely, and then would have slept at mine indefinitely too. Friends make everything fun.

What finally made it all better is that I dreamed about time travel while I was away visiting Tom and then Marie. In my dream, I was standing in outer-space with a man and he was showing me all of these points of light that were events in time. There were glowing threads connecting them and by pulling and stretching the threads, different events could be drawn together and when they touched, time travel could occur. It was such an interesting dream that I fought waking from it. After waking, it made no sense at all, but I couldn't stop thinking about it. Finally in my car, driving down the mountain from Tehachapi on my way home at sunset, it came to me that I hadn't been looking down upon the cosmos, but instead looking inside of my own brain where all my memories continue to glow and burn long after the events that formed them. They are all connected by common emotions, common people, and well, mostly because they all happened to me. While looking at the setting sun, all of my memories both good and bad seemed to draw together into one giant glowing mass and there are so many good things that have happened, that all the bad ones sort of melted away and became unimportant. The kindness of my friends and the love of my family right here and now are enough to carry through time and space to all of everything that ever has been that I remember and make it all good.

A good time to write

2011-04-26T16:05:00.000-07:00

My first royalty check statement ever came today! It is for a book chapter I wrote a couple of years ago. The amount is for $2.48.

I wonder if this means that I am now a professional writer?

I sort of hope it doesn't...
...for a few reasons.

A. It is apparently not a very good profession for me if that is all the money I can make.
B. I don't even know where to find the check associated with that statement.
C. I like having a blog where I can just write whatever I want with no professional expectations.
D. I would rather stay a scientist and just write a bit on the side.

That said, the publishing industry is of growing interest to me. I would like to say that it is because of my little sister Laura's clever incorporation of illustrated yo-yos into coptic binding, but unfortunately, the opposite is true. It is because of the invention of the paperless e-book.

I love e-books. They are all I read anymore (except for graphic novels). Not for any sort of idealogical reasons, but purely pragmatic ones, I think ebooks are amazing. I live in a small city with one book store (A smallish version of Barnes and Noble). It is not nearly as well stocked as the Kindle book store on Amazon. Nearly any book I want, I can have in an instant from Amazon (except for graphic novels and books by Faulkner...because of his estate being opposed to ebooks.)From the book store, I have to usually make a special order that takes two weeks. I like the speed. Beyond that, there is some serious power in ebooks including instant dictionary lookup, instant Wikipedia search, embedded videos, searchable highlighting and note taking. Besides which, one reading device is a lot lighter than a sack full of books.

I find myself trying to implement some of these features into the things I write, for example, trying to find excuses to embed animations in the scientific manuscripts I write. (I am working with some seriously skilled computer programmers these days and they are capable and interested. It would be so cool.) I don't actually like writing that much, but I see so much potential for presenting material in more effective ways than was ever possible before, that I toy with the idea of writing just to test the scope of what is actually possible. I am happy for whatever royalties I can earn, but thought of writing science in new and better ways is the motivation that might actually make it worth-while.

Generation Gaps

2011-03-28T14:56:00.000-07:00

I learned something this weekend that is totally worth blogging about. I was having dinner at the home of some friends. The husband is an attorney. The wife conducts a choir. Sometimes I watch the children of the choir members during practice. She says she bribes me to do so by cooking for me, but we really just enjoy cooking for each other since we both eat gluten free. Conversation with both of them is always excellent. This time, we discussed generational differences in work habits. Which follow:

Baby boomers- Spend a lot of time at work. They feel productive by spending a lot of time working.

Generation X- Spend intermittent amounts of time at work. They have a life outside of work. They feel productive by accomplishing things.

Millennials- The grew up in extracurricular activities and were friends with their coaches/teachers. They feel that bosses are friends and mentors. The feel productive by earning rewards.

When I heard that, a lot of things that had previously seemed crazy suddenly seemed more sane.....like the students who show up to my office hours to "hang out" with me. (That doesn't go over well). And the students who ask me inappropriately personal questions (I guess they seem appropriate to them).

I sort of feel a little bad for not handling those situations more kindly. Not that I was especially mean, more like I just felt I had arrived in the Twilight Zone and was trying to get my feet under me. I was just baffled. I am unbaffled now, and I think I can handle them better.

I sort of wonder what the work habits of the next generation will be. I was running wild with them Sunday evening during choir practice.

My priorities were:

1. Keep them safe.

2. Keep them entertained.

3. Keep them clean.

And I executed those priorities as follows:

Helping the 5-6 year old boys set up a wicked game of basketball in half of the room

then setting up play houses under sturdy tables which kept the 3-4 year old girls safe from flying balls and then giving the 18 month old a lot of supervision / personal protection.

The children were comfortable with those priorities and complied as naturally to them as if that were what they experience every day. I hope that translates well to society when all is said and done.

Selfish

2011-03-22T12:40:00.000-07:00

The best part of evolution (even better than the union of math and biology) is that it revolves around children. Evolutionary time passes in the bearing of children. Every aspect of evolution is hinged on producing children, and ensuring their success. Children are the most important accomplishment a living organism is capable of.

I teach this to my genetics class. I tell them that grandchildren are way more important than children and it's because children don't really count in an evolutionary way until they have reproduced. There are a lot of Hispanic and Hmong students and families are a big deal in those cultures. Many of the students smile and nod in agreement, while others look frustrated and upset, as if their parents are suddenly justified in whatever pressures or injustices they apply on behalf grandchildren.

I think that Christians who oppose evolution are missing out on this. While factions of Christianity rail on about the evil of evolution, they miss this tremendous similarities held in common between faith and evolutionary biology, because children are likewise at the very core of Christianity, ranked with prophets and separated by one degree from Jesus. (Honestly though, I don't know if most Christians realize this.)

In practice, society also revolves around children. Men going to war, willing to die to make life better for their children. Women sacrificing youthful beauty and health to bear and raise children. And they are worth it. After particularly sad funerals, it is little children who draw out smiles and laughter once again. They are the ones who we cook for and keep on trying for when adult problems seem entirely overwhelming.

The perspective that all things revolve around children, seems enlightening when considering human populations. Take, for example early populations of Mormons who practiced polygamy. It is regarded as the carnal misdeeds of a suppressed people, craziness, lecherousness, and generally scandalous. Most people (Mormons included) have problems with it. (Except perhaps certain members of the Sicilian mafia who are reported to be especially kind to missionaries because of their nice suits and historic ties to polygamy. Whatever.)

The journals of those who practiced polygamy indicate that it was a major source of stress, expensive and unenjoyable, which basically refutes the juicier explanations, and leaves many scratching their heads with confusion. From an evolutionary perspective though, the 55 year stint of polygamy makes perfect sense.

While the early Mormons were violently expelled from city after city, many more men than women were killed. The men were shot, whipped, tarred and feathered, and left in the cold to die while the women were merely raped and terrorized. When they were forced from their homes, often in the middle of the winter, men and teenage boys helped women and children cross unfrozen rivers a dozen times in the night, and then died. About three generations of men were severely diminished, the population was small, they were expelled from society in general, and there were quite a few women capable of ameliorating many problems by bearing children. Fifty five years, or about two generations worth of polygamy was enough to grow the population to a less endangered size and even out the gender ratio once again. And then polygamy was discontinued.

Many people who are deeply religious have a lot of children as an expression of their religion. The funny thing about evolutionary biologists (though it may be true of scientists in general) is that we don't. I fall in that category. My evolutionary fitness would = 0 except for all of the nieces, nephews and first cousins once removed etc. (sorry parents, but at least I'm a good aunt). My friend Maria suggested I freeze some eggs down, which would give me an extra decade of reproductive potential, and it seems like a good idea. If I do that, it will be the most selfish thing I have ever done, (though in a sort of evolutionary version of selfishness). And in the meantime, I will apply evolutionary reasoning along with faith and selfishness to the greatest extent I can and keep being a good aunt.

Repetitions

2011-03-20T23:26:00.000-07:00

I have spent the weekend and a few evenings before that tearing apart old jewelry and redesigning it all into newer, more stylish pieces. It has been my catharsis from the lab. In a bout of rage I suddenly decided I wanted to look more girly and wear jewelry on a regular basis. It beats cutting all my hair off which is what I used to do.

We found out last week that a gene had been mis-labled about a year ago and that a couple of months worth of data are shot because the wrong control gene was used. About a half hour before that discovery was made, I was preparing a manuscript and had happily commented that those experiments were forever done. (I had not knocked on any wood. I had been certain and I am not superstitious.) They are not done, but must be repeated once again. Although this time, it will probably take a little less than a month, and the data will probably be cleaner, because the techniques are being perfected by the incessant repetition.

When the discovery was made, I got mad. Really, really mad. I said very little. Only that more care needed to be taken. I did not shout, though I had wanted to. But everyone got really scared. I think I know how my eyes looked. They have been described as wolf eyes when they blaze bright blue like that, but I think they look more like blue flames. Fiery and dangerous. It doesn't happen often. I have never actually seen them in the heat of rage. Only a few hours later in a bathroom mirror. They always look scary, even to me, even then.

And as I felt my grasp of control starting to get dangerously near the point of slipping, I left.

I don't know when I last got that angry. I remember I came close once in Barry's lab when someone started yelling at me for putting the wrong rotor in the centrifuge and ruining his experiment. I don't remember what I said, but I leveled him with two sentences (and a complete absence of obscenities) and obtained the nickname "Smash-tron Miri" from the onlooking undergraduate. (He had known me for three years and was shocked...and a little impressed.) The person I shut down resigned that day. Not because of me he said, but he was at the edge and I think I pushed him over.

As far as my recent bout of rage, well, I had tunnel vision. It took a few hours to calm down enough that I could breath normally and focus on anything. I poured over the data until 9:00 PM, ran statistical tests, became certain of what had happened and the necessity of repeating the experiments. As I did, things started coming back into focus. I realized I was upset about Japan and upset about another professor telling me how angry he is that I am Mormon (which I have secretly been fuming over in my blog for the past few weeks) as well as being upset over the lab. I decided I needed some sort of outlet for all of it. I went home and started stringing beads until late into the night.

They are beautiful. Strands of malachite my Grandparents brought back from the Congo, and bits of ivory, coral beads from Reunion Island, and beads my other Grandma bought from Indian reservations, back in the day when Native Americans sat on blankets in lines stringing beads. Carved stones, and hundreds of silver beads. Things that are difficult and expensive to obtain now, but that were given freely to a beloved granddaughter when I was very young.

Somehow though, I never wore them. They always looked a little dated or too mature or they didn't hang straight, so I pulled them apart and added little bits to update them and even them out. Little specks of silver or crystal, pearls, and new clasps.

In the lab, everyone looked nervous when I came near for the next two days and besides feeling bad about the data, I felt bad that everyone was that scared of me. And when the work was done each day, I came home and put beads together, examined how they looked, refined the assemblies and started over again and again. And each time, the sick feeling of so much lab work wasted diminished a little bit.

The air in the lab finally cleared when I stated that the experiments were going to be redone, but that it wasn't worth arguing over how or when or what had happened and I didn't want to have that discussion. It doesn't matter anyway. I am certain that mistake will never happen again.

And in between work and sleep, I have strung and restrung thousands of beads. The result: I have beautiful necklaces and bracelets to wear and I feel composed once again.

If the new lab supplies arrive in a timely manner, I will start to set up the experiments again this week. I think they will really, really work this time. They have been pulled apart and redone and retested and reassembled so many times. I think every possible mistake has been made, discovered, and corrected. When all is said and done, I think the results will be worth it.

The coolest, nerdiest band ever!

2011-03-17T17:53:00.000-07:00

They Might be Giants came out with with a new album about science called "Here Comes Science"! And there is a Radiolab podcast about it.

My niece Katie watches their videos about the alphabet and at the age of five she saw a bunch of pine trees covered in snow and started exclaiming with delight "Oh what beautiful conifers!" (C is for conifer.)

The podcast is linked below.

Thanks my Mom

2011-03-14T11:55:00.000-07:00

In the past few months there have been several news articles about Merced being one of the stupidest places in the US, one of the most miserable, and one of the most toxic. If there was a survey of Meth-amphetamine production, Merced would score high in that as well.

I am kind of okay with all of those problems. They don't affect me too much. There are some horrible students, but there are some really great ones too, and even the horrible students are among the sweetest kids I have ever worked with. If a survey were taken of least violent campuses, Merced would probably rank among the best. We have had one rape reported in the existence of the University. People argue that rapes are just going unreported, but I have some doubts. I watch the students. They clearly feel physically safe even at night, walking alone. So do I. More so than any other campus I have been on.

I think all cities are as miserable as you allow them to be. (I personally vote for Atlanta as the most miserable.) While unemployment in Merced is high, that is a situation that can be reversed by education. We have a university and there is a sense of hope, at least in the younger parts of the population.

As far as the most toxic....well, the toxins are fertilizers and pesticides used to produce the nations food supply. The toxin levels were computed on a per capita basis. We have a fairly small population and produce enough food for millions of people. Go figure.

As far as Methamphetaine, I don't run in those circles. I did have my car gone through one night and some CDs got stolen. They were mostly burned copies of Beck albums and one from my Sister-in-law's bluegrass band "Miles to Go." There are some houses in Merced that get robbed presumably as a drug related activity, but they are usually in the nicer neighborhoods. I live in a safe neighborhood on the sketchier side of town. The houses there are not a prime target because no one has very much, and there are a lot of cops who are trying to keep the safe parts of the neighborhood from degenerating into the sketchiness.

For me, none of those are huge problems, but there are two major problems with Merced from my perspective....It would be nice if there was more of a 30's something group of professionals to do stuff with, though that is growing. (I have been to several cultural events and a pot-luck in the past couple of weeks and there are more things coming up.) And it would be nice if we lived closer to the service providers for lab equipment. It usually costs more in travel expenses to bring in repair people than the actual repairs cost.

As a result of the trouble and cost of bringing in repair people, I am periodically asked to help solve mechanical problems. (Usually not by men...but even that has happened a few times.) Which seems weird because I can't think of any breathtaking act of tinkering I have ever done that has saved the day or anything like that. I am occasionally successful though, and I have never made a problem worse. I have successfully built some things, diagnosed problems and connected water pipes. All of those things seem pretty obvious though.

But maybe they aren't to everyone. It has occurred to me that my mother may have prepared me exceptionally well for life in Merced. She is a tinkerer and can capably repair a small engine. When I was growing up, she always had me engaged in some project in which I was developing mechanical, construction, repair, or other skills. She has taught me to respect all people, including the uneducated and the poor. She also taught me the value of education. And she has taught me to love growing plants, farming, and gardening. Finally she has taught me to not leave valuable things in the car. (Though that was sort of a side-effect of some of the worrying that leaving items in cars has caused her.)

Thanks Mom, for raising me to enjoy my life in Merced.

Connected

2011-03-11T11:56:00.000-08:00

My sister Laura called yesterday because she was feeling anxious. She is at the end of school, about to graduate. She has a major design exhibit of her own work to pull together. Reasons upon reasons, but none of them seemed to her like THE reason. At the exact moment she called, I was also feeling anxiety for no definable reason. (Our lives seem to be strangely synchronized.) I know what triggered it. A friend stopped by my office to chat briefly but looked at his watch every 10 seconds or so whenever I was talking. Normally, that sort of behavior doesn't rattle me, but somehow it did yesterday. But it wasn't just that. There was more lurking beneath.

I think it all started a couple of weeks ago when I read a post on Kottke.org about the loneliest creature alive. There is a whale that sings at a unique pitch, different from any other whale and so it swims the oceans alone. That sort of struck a chord with me because, while I am certainly not alone in my life, I often feel unique. I have never met another female, Mormon evolutionary biologist, especially not in the sub-specialized areas I research in, which tend to male dominated and atheist dominated.

The female and the Mormon parts of my life make it sometimes difficult to interact with evolutionary biologists. The evolutionary biologist part of my life sometimes makes it difficult to interact with Mormons. The Mormon and the evolutionary biologist parts of my life make it difficult to interact with just about everyone else. If these populations were represented in a Venn diagram, the place where I fall would be tiny, just a point.

As I write this, it rings true as the source of my inexplicable anxiety yesterday, during which Laura called.
And we talked about things to cheer us up: make-up, corsettes, friends, her upcoming exhibit, but none of them seemed to help that much. In the end, we mostly talked about Paul Erdos. He was a mathematician who did not connect well with people, and instead became a friend with numbers. He went around helping the numbers being clumsily handled by other mathematicians, and when his work was done, he would leave and move on to the next set of numbers in need. I don't know if he ever had close human friends. He existed in an even more obscure part of a Venn diagram than I do.

The irony of his existence is that people now compute Erdos numbers, which is how many degrees of separation there are between themselves and Paul Erdos in scholarly publications. It is cool to have an Erdos number and therefore claim some connection to the man. I don't have an Erdos number yet, but I bet when I finally publish with Kristina Crona, I will. I look forward to that.

Another thing that Laura and I have discussed lately is the purpose of our blogs. She has finally figured out the purpose that hers has served which got me thinking about mine. And I think I have figured out what mine is to me. It is a place where all of the crazy categories that define the point of the human population that I live in can come together and be socially acceptable in a place that is public (sort-of). As there are currently 13 followers of my blog, and a few others who chime in from time to time, it confirms that while my little Venn space may be unique, it is certainly not isolated.

Good Science

2011-03-10T15:01:00.000-08:00

Merijn Salverda just published an excellent manuscript about adaptation and he used the TEM gene as his model for the study. I smile so much because of this paper. First, it is top-notch science, published in a good journal. Second, Merijn and I have been discussing the evolution of TEMs since we were both grad students. It is nice to see all of his work finally in print. Third, the TEM has become a model system for studying evolution.

TEM is an important antibiotic resistance gene that confers resistance to penicillin and a few related antibiotics. It evolved the ability to confer resistance to many many more antibiotics. I decided to make the TEM gene a model system for studying evolution when I was a student. Although, I cannot take all of the credit for that happening, I have been a part of it. Palzkill and Stemmer came before me, and Weinreich and Salverda have made invaluable contributions applying the gene to basic population genetics. TEM deserves most of the credit because it is so amazingly adaptable, and along with the gene, the many clinical scientists who have recorded the clinical evolution of the TEM descendants.

My own contribution to the cause has been my willingness to dance between the two (often opposing) cultures of medicine and evolution, and do science that is meant to be simultaneously and equally valuable evolutionarily and clinically. Most clinicians do not value evolution as a practical tool, and most evolutionary biologists have a fairly low regard for clinical studies (until they get sick). I have respect for both. I was once a pre-med and a good one. I could have gone to med school. I studied the immune system and epilepsy. But ultimately, I decided that evolution had better and less bloody tools for answering the questions I wanted to ask, which turn out to be health related.

There have been a lot of fights to convince opposing sides of the value of each other. The first phylogeny I published in a medical journal was strongly fought against by the reviewers and editors. I fought back. Evolutionary biologists have thought my work is too clinical to be important to them. I am still fighting back. Merijn's paper will help.

Doctor's Note

2011-03-08T12:35:00.000-08:00

In a couple of months, I will babysit Tom's children for a week. This is an intimidating task. They all love me, have fun with me, think I am pretty cool, and are always excited to see me. We make crafts, cook and learn about science together. But a week is a long time, and at the pace I go, that is a lot of stuff to plan.

So far I have planned building wooden dinosaur skeletons, going the the Natural History museum, hiking with field guides and giving age appropriate discourses on the flora and fauna we observe, paper chromatography, the zoo, 3-D paper crafts (because Mattie will insist whether it is planned or not), and probably some You-tube videos about DNA replication and evolution (again, because Mattie will insist on learning more about what I do in my lab). Since there are three girls and one boy, I think that these activities are good because the girls will enjoy them, and so will Sam.

But then, I found out that the children will still be in school, except for Hazel who is too young. If all of the children were going to school, I would be okay with it, but me and Hazel one-on-one....hmmm. Hazel has not always liked me. She started liking me when I asked if she wanted me to swing her upside down. At first she said "No!" and ran away to Tom and hid her face. After considering it for a few minutes, she decided it sounded like a good idea. (These kids have uncles, on the other side of the family, that do backflips over fire and dive off of really high cliffs. It is in their blood. They are fearless.) So I picked her up by her ankles and started swinging her a little. She started pumping her torso, trying to swing higher and saying "higher, higher!" So now we have a relationship based upon my swinging her upside down and scaring all present adults (except her parents, who approve). I can safely do that for about two minutes and then my arms get too tired. So if I am going to be hanging out with Hazel a lot, I need to find some other Hazel friendly activities. (The other children would not forgive me if I took her to Legoland without them. Anyway, she is too short for the rides that leave you swinging upside down.)

I would like to pull them all out of school, but they can only have three absences without a doctor's note or else they are considered truant and legal action is taken against their parents. I am a doctor (of sorts), and so I would like to write a note, but I doubt that is what the school means. I might try anyway (if their parents go for the idea). My friend Shona once said that she would think her Ph.D. was worthwhile if it ever enabled her to afford a pair of go-go boots. I think perhaps mine will be worthwhile if it enables me check my nieces and nephew out of school.

Cooking

2011-03-06T21:04:00.001-08:00

I was Barry Hall's first graduate student in 15 years, his third ever and the last one he took before retiring. He said he thought I might be worth taking because I had fire in my eyes. He was also impressed with my cooking. He said "Most good scientists are also good cooks. If you can do science as well as you cook okra, you will be great." (Mine was the only okra he had ever eaten up to that point. I have cooked okra exactly twice. The second time didn't turn out so well, but that was over a year later and Barry liked my science well enough to let me stay in his lab anyway.)

I I have thought about that wisdom as I have navigated a gluten free diet. I HATED giving up gluten, but I hated being sick all the time a lot more. My mantra has been "Once you give up the expectation that food should taste good, it really isn't so bad."

Eventually though, good food emerges. For example, quinoa pilaf with caramelized onions, pine-nuts, mushrooms, squid rings, mussels, scallops, and shrimp has been a favorite when served to a crowd making the choice of what to eat out of desire alone. Cakes and cookies are fine too. No one can tell the difference. Flan is divine and although tapioca draws strange looks, people enjoy it too. But bread, that universal staple, has been hard. It has usually seemed like jet puffed pad-thai, or a slab of baked oatmeal. I have thought countless times, If you can speed evolution up in the lab...if you can identify bacteria by denaturing them...you can find some way of making bread that is enjoyable to eat.

It has taken over a year, but tonight, I succeeded and ate bread worthy of being called "bread". It is especially good with extra virgin olive oil and salt.

I am hopeful that the molecular biology in the lab will go well this week.

Impatient

2011-02-27T16:26:00.000-08:00

The weather keeps teasing me with the prospect of spring.

I think it might really be getting here this time.

Presentation Problems

2011-02-26T19:31:00.001-08:00

A while ago (I can't find the post), I posted a blog entry about measuring circles. I was moaning because there were so many to measure and the smell of the bacteria that formed the circles made my eyes water. I moaned a lot more later, (though not publicly) because after measuring all those thousands of circles, the data just didn't make any sense. It turned out there was a problem with the agar and the whole experiment had to be repeated.

Enter Christiane Goullart, my brilliant graduate student, who repeated the experiment. It worked this time. The cursed t-tests that drove us to measuring thousands of circles came out significant (for the most part) and now we have glorious data that make sense. To be exact, we have 64 Excel spreadsheets worth of data.

The data are hot. They describe 32 naturally occurring adaptive landscapes which show how numerous antibiotic resistance alleles have evolved. I have described these data to population geneticists and they are in awe and amazement. The Berkeley math department is also in awe and amazement (though I still don't understand the exact reasons why. It seems that they have some new basic math that they are discovering to describe adaptive landscapes, and they want to use my data because they are a reasonable representation of a small slice of reality.) Kristina Crona, the resident mathematical genius used to be in awe and amazement, but now she just wants the data published. We all do. But we have a major problem. How do we describe 64 spreadsheets worth of data and analysis in a single manuscript? (Which is what we think we should do since it all tells one story.) Or if we break it into separate manuscripts (we have outlined six if we go that route) How do we tell the whole story? And finally, once we make the story tellable, how do we fit it into a half hour presentation for Christiane's qualifying exam committee, especially when that committee will probably consist of an organic chemist, a computer scientist, and a bioengineer (but no evolutionary biologist).

I guess that this is a good sort of problem to have, but I kind of wish there were holographic journals that included 3-D animations of data. Unfortunately, there aren't, so were are trying to pull this off with Mathematica and 8.5" x 11" paper. (Sigh)

Ravens

2011-02-22T22:07:00.000-08:00

When I moved to New York for graduate school, one of the oddest challenges was finding a place to deposit money. I simply didn't have enough to reach the minimum balance of any of the banks (which was $1500). It didn't seem likely that I would save that amount in any reasonable amount of time, considering that my stipend was $800 per month (before taxes) and half of that went to pay my rent for the tiny studio apartment I lived in.

Not having a bank wasn't as much of an inconvenience as one might think. I lived downtown, in an old hotel that had been turned into an apartment building, mostly for students. It had been a luxurious hotel, and where the paint was peeling from the doors, intricate patterns of inlaid wood were visible. Mostly, the apartments were the dwellings of music students and at night I could hear my next door neighbor practicing the cello through the wall. It was like eves-dropping on a concert, she was so good.

As one might imagine, an apartment building inhabited by such a cultured population was in the center of everything. There were routinely city festivals right in front of the main doorway, and as alcohol was routinely sold at those festivals, I was routinely carded just to be able to go home at night. One night such a festival was taking place while my dad was visiting (he was on a two week business trip to Binghamton and came up for the weekend). On that particular night, about half of the graduate students in my program were partying down in the street, and they decided to come up and pay me a visit. They all came to my door drunk and with plastic cups of unknown beverage in their hands. I warmly welcomed them in, but no one would step though the door way. They all apologized and left. I later asked César about that. He said, "Kiddo, it wasn't just that A dad was there, it was that he was YOUR dad." It still didn't make any sense to me. My dad is just about the kindest man alive.

In such a cultural hub, things worked out pretty well on a strictly cash basis. The apartment manager had no problem with cash payments for the rent; the utilities company was about two blocks away and they liked cash too. There was a thrift store a half a mile away where I found all my furniture, a farmers market where I bought my food just beyond that and I lived about two blocks away from the bus station where I caught my ride to school. All those establishments seemed to prefer cash. The bank where I cashed my stipend checks was about four blocks away. They informed me that they preferred cashing checks for people with accounts at the bank, but as the checks were drawn from that bank, they had no choice but to cash them. (When I finally found a financial establishment that would allow me to deposit my meager finances, it was a credit union for artists. The minimum balance was $5.00. I wasn't an artist, so I joined a community darkroom, which was basically a co-op for photographers. That also cost $5.00. But that came later.)

My older sister Marie loves giving me strange gifts. (Before the airlines were so strict, she would give me things that could not be packed in a packed in a suitcase, and while not illegal in any way, were also not traditional carry-ons. She enjoyed seeing how I would rise to the challenge. One year, she sent me on a plane with a topiary made of ivy and a cast-iron footstool. I told the person at the check-in desk that I wanted a little ambiance. And honestly, several travelers sat near me during the layover enjoying that ambiance.) I got a package from Marie with a mug in it. It had a new-agey message about how DNA is the thread that unifies all life. The genetic code was printed on the other side. I decided to take it to the lab with me and I caught a bus to school. About three hours after arriving at school, I got a phone call from the bus office with someone telling me that my wallet had been turned in, but that everything looked in tact, so I shouldn't worry too much.

It turned out that the bus office was also a short distance from my apartment, so I went on my way home thinking about friends whose wallets had been stolen and remembering their words "I wish they would have just taken the money and left the rest there." And as I collected and opened my wallet, my heart sank because that was exactly what had happened. I had just cashed my paycheck. Thankfully, I was payed bi-monthly and this wasn't the rent check. I had paid the utilities and even put money on my copy card. But I didn't have much food, and it would be a whole month before I would be able to afford any more.

I went home, and listened to the cello playing through my wall. I thought about Elijah being fed by ravens. I laughed because I was no where close to hungry enough to eat carrion from a bird's beak. A person would get parasites or a disease eating that sort of food. I thought about the Israelites eating manna and I was certain I wouldn't eat bread off of the sidewalk either. I cried a little and took a shower and went to bed.

The next morning I got up and headed back to school. When I stepped outside, I noticed a dollar on the sidewalk. I used it to buy breakfast from a cafe next to my apartment. And the next morning, a five dollar bill was there. It was Saturday and I went to the farmers market where a person could buy three pounds of just about any vegetable for a dollar. On Sunday, a dollar was once again on the sidewalk, but there were two women walking towards it and they were closer than I was. I hurried as fast as I could, but they reached it before I did... and then walked right over it, like they hadn't seen it. I started feeling a bit guilty. People were losing the money that I was finding. I didn't want to be a thief, or even feel like a thief. But then a different thought struck me. It was that there was lost money blowing in streets all over America, and that the street money was just being disproportionately represented in front of my apartment and that no one else was really interested in it. Well, that worked for me.

I was always sort of surprised that the money was there each morning, but it was there for over two weeks. It didn't matter if I left at 6:00 AM or 8:00 AM. It was there. And then one morning, I was tired. (Graduate school is exhausting after all.) I woke up at 7:00 and instantly thought about the street money, but then I realized that there was enough food in my house to last the remaining week and few days and that I would rather sleep a while longer than pick up some money. And I knew that I didn't need it any more and that it wouldn't be there any more. I wished it well as it blew its way on to some other person in need, and I never saw money on the sidewalk there again.

I have been thinking about that ridiculous situation I was in as I approach going up for tenure once again. I am a little scared, and I think about alternative careers, like being a tambourine player in a band, or becoming a physician's assistant. There is a part of me that thinks I should not allow further schooling to even be an option. I spent a lot of years in school getting my degree, and apparently liked it so well that I became a professor and stayed on. I worry that there might be something wrong with me if I forever consider school to be my solution to everything.

And then there is the part of me that has hope. Maybe I will get to keep being an evolutionary biologist, which is what I love best. Since having my tenure package sent back to me to work on for another year, I have found friends I didn't even know I had. And they have helped me with grant writing, data gathering, computer programming, equipment purchasing, speaking opportunities, organic compound synthesis, and experimental design. I would like to think that there is something I have done to deserve all of this, but I don't think that is possible. I think there are just a lot of very kind and intelligent people in the world and that somehow, they are disproportionately abundant in my life.

There are some moments I love UC Merced

2011-02-16T12:56:00.000-08:00

This is my walk from the parking lot.

Happy (Valentine's) Day!

2011-02-14T17:04:00.000-08:00

I used to celebrate the day by chopping raw meat (for stir fry) and watching X-files with my best friend. Then it became just another day for a while or a day for really awkward dates. (It's just causes too much pressure.) This year however, I am celebrating like CRAZY. I did not give or get flowers, chocolates, jewelry or any red hearts. (Though there was a cute mad-libs Valentine card taped to my office door this morning. It even came with a pencil.) I did better than that.

This year, for Valentine's Day, I got two calorimeters. They were not technically a gift from anyone, but the random and lucky circumstances that enabled me to obtain them, and the numerous people who contributed towards their purchase make them seem like a gift from the gods. I have been trying to obtain those calorimeters for four and a half years. I have tried to collaborate with people, to obtain venture capital, to get grants and prize money, and I have written business plans. None of it has worked, and yet, I have finally obtained them.

The reason I have wanted them so badly is that I have patented (pending) a method for identifying bacteria, and another for determining their antibiotic susceptibility. Each method requires a different calorimeter and they are fairly expensive instruments. I finally located some used ones that are clunky looking (like 1980's technology) but they are really sensitive, and cost much, much less so I don't actually care.

Everyone I talk to about this method thinks it will work. They all think it will be a multi-billion dollar money making product. The problem with that is that most of the highly impressed people try to go forward with the method without me, hoping somehow that the patent-pending status will never become an actual patent. I decided that saving the lives is my real priority and so I don't get too upset when people try to rip it off, but I also don't help them in that endeavor either.

Sometimes hick-talk (a vernacular phrase for "vernacular") comes out of my mouth, especially when I am answering unexpected and difficult questions rapidly, which kind of causes people to underestimate me. (Come on, I am first generation Ph.D. in my extended family at large on both sides and vocabulary was not emphasized in my schooling. I am working on it.) I don't care too much when people at large underestimate me, though it does hurt some when funding is on the line. Regardless of what anyone thinks of me though, I have kept a few aspects of the method proprietary, and while they are un-patentable, they are critical. Remarkably, I have been smooth enough that no one has realized anything proprietary was happening right in front of their eyes while I was demonstrating the method. (Or else I am just generally so awkward that any additional awkwardness was not detectable.)

Anyway, it's my turn now. I get my own shot at developing the technology I came up with (with a couple of awesome co-inventors who will be duly credited in the first manuscript, but who may not be enthusiastic about appearing in a blog entry) and it feels absolutely wonderful.

Sometimes naked seems like a great idea except for the being naked part

2011-02-12T19:33:00.000-08:00

I have run out of clothes. This has become apparent from the occurrence of my wearing high heels to the lab four times last week. On one of the days I was in nude 5 inch stilettos with a nude silk skirt. What was I thinking?!

I shrank a size and all my clothes were falling off. That's the main problem, and I'm still shrinking so I thought I'd try to skip buying a whole wardrobe in my current size and just wait until reaching the next size down. I have three pairs of inexpensive jeans and some t-shirts that more or less fit. I also have skirts, which are great because they have a large distribution of sizes over which they can be worn and look acceptably okay. (They are bad because they cannot be worn with tennis shoes.) I was hoping that would suffice for a while, but I gave up. It turns out that shrinking a whole size takes some time. Aside from not being as diligent with diet and exercise as I ought to be, it is also because sizes are normally distributed with a fairly large variance so it takes a while to get solidly out of one size and into the next.

Going clothes shopping requires leaving the city of Merced. That is because fashion here is centered around two things: blackletter and bling. I do not care how popular those two elements of style are in Merced. I will not comply. I am clueless enough that I would inadvertently wear gang attire in the wrong part of town and end up dead. I go to Modesto or Fresno for most of my clothes. (I would buy them off of Amazon it it weren't for the variance in size problem.) Neither Modesto nor Fresno are exactly hubs of fashion, but I don't need to wear runway fashion in the city of Merced, so they suffice.

However, before embarking, I research try to get an idea of what styles exist outside of the Central Valley for those happy occasions when I journey to civilization. Research always includes one thing: buying the latest issue of Vogue to see where things stand. It has clearly been a while since I have looked through a fashion magazine, because most of it looks hideous to me. Tangerine is not a good color for many people (like me). Paired with red and aquamarine, it only gets worse. The daisy dukes the models were sporting were supposed to be reminiscent of gym shorts, but they looked more like granny panties to me. And then there were also the models themselves. Fashion has once again moved away from classic beauty to more mannish looks. I was sort of okay with it until I turned to a page where the model bore a striking resemblance to teenage photographs of my dad. She was slightly less masculine looking. (I am deciding whether to bring those pictures to family reunions and try to fool people into thinking that my dad wore drag. Hmmm.... It's a bad idea, but the resemblance is strong enough it would probably work.) Yikes!

Thankfully Chanel and D&G pulled through with some wearable stuff, and while I certainly don't dress in those brands, at least there will be some reasonable knock-offs.

David Fullarton

2011-02-09T08:28:00.000-08:00

I love this. His website is here.

Media Wars

2011-02-07T17:51:00.000-08:00

I used to watch Bones, but honestly, all the dead bodies were getting a little depressing even with the snarky humor. And then they went after Mormons. I mean, it wasn't totally hard core all out open warfare like Tom Hanks or something, but still, it was just so 1840's. Okay, that may be optimistic. The last law promoting the slaughter of Mormons was taken off the books (in Missouri) in the mid 1970's. But that is still over 30 years out of fashion. Not cool.

So I moved on to Flight by Sherman Alexie and it is about Native Americans and violence. Definite slaughters in that book (audiobook style...so I can listen while I do mindless tasks.) Now, it may be this acne drug I'm taking that lowers androgen levels rather than the book, but I just keep bursting into tears. I probably won't finish it. I mean, I give it a rest for a few days, but within 5 minutes of resuming, tears are freely flowing. Freaking hormones.

(I should add that Merced just finished up a month of dense fog. No sunshine. Mist all around even in the middle of the day. For a month.)

So I declared war on depressing media and I listen to The Bangles a lot now. I think it is impossible to be sad with "Walk Like an Egyptian" playing in the background. (Oh, except wait...)

Oh well, at least the sun came out again.

Happy me.

Waiting games

2011-02-04T16:13:00.000-08:00

I stopped going to faculty meetings over two years ago. I made the decision while hyper-ventalating in my office after a meeting where they told us that some of our space would be taken away to accommodate new hires. Then they showed the hiring plan and the space taking away plan, and I was going to be the first one to be hit. Technically, it was the whole suite, and not just me. There are three lab groups per suite. I am situated between the two largest and best funded groups at UC Merced.

The main thing discussed at faculty meetings (when space isn't getting cut) is the hiring of new faculty members, and I decided I didn't want to hire any new faculty members. Aside from the obvious space issue, I was involved in something like 15 faculty searches in my first three years. I had done my share of recruiting and I didn't want to anymore. The consequences of that decision are outlined above, and the result: I still have all of my space, (I am not sure why since I don't go to meetings, but I think it has been really hard to recruit future faculty into space that they can't see and are only told will be taken from their future colleagues. Although it might be because they actually crammed four faculty members into one suite and it didn't work out so well. One of them just left and her space had been taken over before the door closed behind her.)

I think my attitude caught on a bit because for a long time, faculty meetings happened quite rarely. Only two or three times a year. But they are starting up again. This time, it is because we are forming departments. I have been assured that these meetings are important, but again I am opting out. They sound like the space meetings....people getting excited, emails flying furiously, not much action. However, this time, in the end, there may actually be a bit of change. We might actually have departments, and if I am required to, I will choose one.

They will all want me. Teaching credits and student interactions are the currency being fought over, because the hiring of new professors is based on professor/undergraduate ratio. I teach genetics, which had 96 students last semester. It will probably have to be bigger the next time I teach it since we are growing by ~800 students per year and most of those students want to major in something biological. And I also teach human biology. There were ~70 students in that class last semester and it will probably get bigger too. I used to teach microbial evolution with a measly 8 students (until the dean cancelled that class), and even then, I was coveted by various groups because of my genetics course.

When I think about what department I would want to be in, I actually think it would be chemistry. The only problem with that is that I'm not a chemist. My reasons for wanting in: I actually like most of the chemists and I think they would leave me alone and let me get work done. I have discussed with my faculty friends that we should form the "Just leave us alone and let us get some work done" department, but it would backfire. We all teach pretty big classes and so the new faculty hires would all come to our department. All that hiring would destroy the concept of Leave-us-alone-and-let-us-get-some-work-done. So I'll just wait it out and pick whichever one seems best if departments ever actually form.

Nerd chic

2011-01-27T21:43:00.000-08:00

Sometimes, I think that I should blog about what it's like to be a scientist, trying to figure out how to dress well and not smudge make-up but who is nerdy enough to wonder if make-up and clothes really matters to bacteria anyway. I think many scientists are like that. We are still trying to figure out, well not exactly how to be cool, but how to at least be savvy and well respected. We have stories that get displayed like scars from battle wounds: Fights with jocks, fights over doing too much homework, fights with egomaniac nerds. There is one scientist I know who is a nerd by choice. She went both ways....meaning cool and nerdy. She was a child model and appeared in pudding pop commercials with Bill Cosby. She was very cool as a kid. She still looks fabulous always. She is a nerd and very cool and nice and the university always uses her for P.R. I tell the school that if they want me to do P.R., I need 24 hours notice if they want a guarantee of the hair and nails being done and the clothing matching.

I have friends who know more about clothes than I do. They give me suggestions. And I do research of my own. I am researching hair extensions these days, on-line. I also went on a field trip to Sally Beauty Supply to see some in real life. Everyone says that Sally extensions are junk, so I didn't buy them....I only looked. I found a House O' Hair in Oakland that sells thousands of wigs and extensions and I am definitely going there. Extensions are sort of my new hobby. I have watched numerous You-tube videos about them and they were pretty helpful. That is until I got to one with a drag queen showing how to apply extensions with liquid latex, and in rather crude terms angrily assuring the viewer that the latex doesn't damage hair. That one might have been useful, but I kind of felt assaulted by it so I didn't finish.

I kind of teeter totter on the grooming. I always bathe, that is not negotiable. And my New Year's resolution was to wear mascara every day. (I have missed twice so far. ) But the nice clothes, lipstick and hairspray definitely get forgotten when I get busy, especially grant writing busy. I mean, one can write a grant in pajamas...and yet, after a few days of slugging around, writing, and introspecting, I dress up simply to feel good. So much of who we (scientists) are is inside...what we think about, create, plan, and analyze....and maybe sometimes, we overemphasize the importance of our brains. Maybe we need to worry about clothes and hair and makeup simply to achieve balance between what is inside and what is out.

coming back

2011-01-18T15:37:00.000-08:00

I exceeded my legal limit of chocolate (which is none) this Christmas. It's amazing what a dozen M&Ms a day for a week can do to a person with a very low chocolate tolerance level, but I think I am finally back. My friends all say that they are jealous of my response to chocolate, which is short term memory loss and a sort of euphoria. They think it is a great way of mentally escaping the holidays through inexpensive and legal means. I couldn't really say. I don't remember.

Now I do remember Christmas day and what skiing in powder feels like and that I want to do that some more. The cabin we stayed in was lovely as was snowshoeing and time spent with my family. I didn't head into chocolate until about the 28th or 29th. New Year's eve is vague, but as it was some awful dance party where most of the people were way too old, it is best forgotten. After that, not so much at all. I left my coat and shoes behind at my parents house and a collapsible cooler that was headed for the trash. I sort of miss the coat, but I'll get it back on President's day, so that's all right.

Somehow, science never gets lost, even in the hazy midst chocolate that causes me to get turned around and lost, and forget to sign things, and trail off in conversation, even then, science doesn't shut down. It's the part of my brain that is most consistent. And with the science part of my brain, what have I done lately?

Well, busily writing a grant and training two graduate students. And also gearing up for some hot science in my lab. Literally. I'll be melting bacteria.

There is this patent. I have had it for a few years and I'd like to license it. It describes some new and really fast ways of identifying bacteria and determining their susceptibilities to antibiotics. The only problem has been that I didn't own the equipment necessary for doing the studies and I no longer had access to the equipment I once used. However, after pursuing every option and beating down doors and pitching this project, I am finally getting the equipment I need and I will own it. It is used and the casing is dated looking, but I don't care about that. It does what I need and that is what matters.
I like the idea of saving lives.
I like the idea of patent royalties.
But the main motivation behind this project, that I am a nerd and just want the chance to do this science.
This project has been declared dead a zillion and a half times, but it somehow always reemerges and it is finally coming back in full force.

Cat and Girl

2010-12-16T20:46:00.000-08:00

I got introduced to this website today.
http://catandgirl.com/ (It is strange and wonderful.)
There was a comic from it in my email this morning and I laughed about it over my bowl of Chex. (No milk came out of my nose though. : )
I want to share it and make others laugh too.
(And if milk comes out of your noses...I won't laugh. I promise ; )

Good Grammar (?)

2010-12-09T08:52:00.000-08:00

Rules

2010-12-08T10:20:00.000-08:00

I am basically a self governing being, but I don't mind authority or being told what to do, when what I am being told to do makes sense. I am pretty generous about what makes sense. I will follow rules to maintain order, to keep the peace, to protect people's feelings, to be safe, to be honest, to be moral. All of those rules makes sense at least a little.

UC Merced has a lot of rules. We used to not have any rules and I liked that. Work was more spontaneous in good and bad ways, but there was also a lot of flexibility. At some point, someone at UC Merced decided that we need rules and so everyone in an administrative position started making rules. Those rules require making other rules for the sake of internal consistency. Then there have to be other rules to make those rules enforceable. In the past couple years, UC Merced has been slammed with a tsunami of rules. Most of those rules do not make any sense to me.

For example, a prestigious scientist would like to be an adjunct faculty member here. She helps with teaching, co-advises graduate students, and collaborates with faculty. She does all of this for free. And yet, every two years, she has to go through the same rigorous reviews that all pay-rolled faculty go through. This makes no sense. I am always responsible for writing up her case and I do it because I like her. I want her to be able to continue being adjunct here, but the process is insane. I complain to every person in the ladder of review about the insanity of this in hopes that it will go away. It probably won't.

At UC Merced, there are a lot of people whose jobs are mainly centered on rules and making sure they are kept. The UC is also in a budget crisis. I think if we eliminated 50% of the rules, the University could not only eliminate the need for so many rule enforcers, but it would also become more efficient and a better university, since people could focus on what is important rather than jumping through all of the regulatory hoops. That is my plan for balancing the budget (It won't pass). It might work on a national level as well as a UC level. If I were to run for political office, my platform would be to start eliminating unnecessary rules.

That said, in my lab, we have just come up with our first three rules.

(Besides: DON'T BREAK THE CENTRIFUGE! and PUT ENZYMES BACK IN THE FREEZER! which are really more like laws enforced by the death penalty.)

1. ) No thigh high boots in professional situations. (I think they are awesome and I dearly want a pair, but everyone says they are a bad idea. I am sure they are right....but what about over the knee boots? Aren't those okay?)

2.) No chair dances during talks. (My graduate student may have watched a little too much Liza Minelli. She not only picked up the charisma and confidence; she also learned the chair dance. eesh!)

3.) No making a profit off of people contributing funds towards the purchase of equipment for my lab. Contributions cannot exceed the cost of equipment. (It would be immoral.)

I think that is probably about enough rules and that it is a good list.

Don't you want me to run for political office in your town now?

It ends with a bang! not a whimper

2010-12-06T21:05:00.000-08:00

This semester is not winding down. Classes end Wednesday, but the end of my work is nowhere in sight. Writing....always writing, a conference in Irvine, and a much anticipated sexual harassment play (?).

My sisters keep me going. I call them when I am freaking out, or when I have had a good day, or when I miss them (except not always when I miss them, because I always miss them.)

(Cute Marie having fun.)

(Marie and me making stock photos for the hotel...too bad they didn't want them.)

(I like this one. It looks epic)

(Laura laughing about our matching sushi pajamas)

(Laura describing her best kiss ever.)

I am glad that I got to spend a fun weekend with them in San Francisco. I cannot wait to see them again. It is what I am looking forward to and a light is shining brightly enough at the end of the tunnel, that even though I can't see the end, I can feel the warmth of it waiting.

Brain power index

2010-12-03T22:14:00.000-08:00

Merced was just ranked the least brainy city in America. Visalia and Bakersfield (nearby cities) were in the bottom five. It sort of causes a shock to see that in print. I waiver between near-violent hatred of that study and extreme fatigue. I am certain it is true. I live it every day.

I like it that there are laws about how many chickens one can have as pets. (Not to be slaughtered and eaten; that is illegal.)

I don't care if the grocery stores where one shops are a status symbol simply because there aren't any other ways people have of saying they are in the upper echelon. (I do most of my shopping at the Mexican ones... they have the most interesting food. And yes, some people are nervous about eating my food when they hear where it comes from.)

I can handle that almost all the other women my age are single moms. (They are quality people doing the best they can.)

It hurts when kids don't think they can go to school. (They are as smart as anyone anywhere. Sometimes when they see that school is a possibility, they get interested.)

It almost kills me when their parents try to stop them. (Some people just don't have any sense.)

And some us are trying so hard to change it.

I give everyone between the ages of 14 and 18 information about financial aid and explain it to them.

There are a few students who I have perhaps influenced a bit to leave and go to college elsewhere.

And there are some brilliant students who stay and become my students and blossom.

Blue collar mood

2010-12-03T09:49:00.000-08:00

If I could do anything I wanted, I would stay home today and re-floor my bathroom. It looks like a truckstop from the 1970s even when freshly cleaned. And while I guess I could technically play hooky today, it would be highly irresponsible. I finished a manuscript yesterday. It is almost ready to submit. But there is still one more grant application to write, two more manuscripts to write, a stack of exams to regrade, and two final exams to write.

I used to love wood working and do it at every chance I got. I still like it, but I don't have so many chances. I used to do quite a few home improvement projects (at my parents' home) and I professionally (?) landscaped homes and commercial sites to pay my way through college. I loved that kind of stuff.

When I was in high school, writing was the thing I was worst at. In college, my creative writing teachers liked some of my stuff, but my essays in science classes didn't always do so well. I would lace them with humor, fact, hyperbole, metaphor, and sarcasm. In graduate school, writing was my Achilles' heel and I had to get rid of the literary devices. Absolute torture.

I used to never want to be a writer when I was young. I went into science to avoid it. Now I am mostly a writer:
When problems come up, I write. (grants and such)
When results come up, I write. (manuscripts and such)
When I have free time, I write. (blogs and such)
I think I kind of love writing.

Somedays though, manual labor sounds really appealing.

Wade Alexander, Tyler Berg, and me, taking a break from building a water line down a mountain in Bolivia. It was my most recent encounter with real manual labor.

How to make popups

2010-12-01T13:23:00.000-08:00

This has nothing to do with antibiotic resistance, but it is the coolest thing ever! Robert Sabuda has templates for making pop-ups on his website. I hope you enjoy!

Finding a larger forum

2010-12-01T11:23:00.000-08:00

I started blogging about antibiotic resistance because it is an under-appreciated problem. It is alas, despite my best efforts still an under-appreciated problem. I started writing content for factoidz because I think I might reach more readers that way. I will still keep blogging, but I will also start posting links to my factoidz articles. Here is the first.

Worth reading

2010-11-30T14:34:00.001-08:00

This is good:

http://www.foxnews.com/scitech/2010/11/26/secret-agent-crippled-irans-nuclear-ambitions/

Lovin' Liza

2010-11-30T14:21:00.000-08:00

The strangest homework assignment I ever got was to rent some Liza Minelli movies and just watch them. I was learning how to give a scientific talk and it was going so-so. I couldn't project my voice, I forgot key phrases and my hand gestures were self conscious. Barry assured me that Liza suffered from none of those symptoms of stage fright, that she was the best, and I needed to learn from her. So I did and I won a speaking award for the talk I gave. I became a grateful fan of Liza Minelli that day.

Now I am the one with graduate students and I am once again grateful for Liza as I teach them how to give talks. She really is amazing.

Give and take

2010-11-29T21:15:00.000-08:00

There are some days when science is wonderful. Today was one of them.

Videojug continued

2010-11-27T20:39:00.000-08:00

I decided on a videojug topic: How to Prevent Antibiotic Resistant Infections.
I discussed it with Tom over lunch today. Between the two of us, this is what we came up with:

1. Avoid close body contact with people who may have bacterial infections.
2. Don't wrestle.
3. Clean gym equipment before using it.
4. Disinfect cuts and abrasions.
5. Don't get admitted to the hospital, especially the ICU. This means staying healthy.
6. If you are in the hospital or a doctors office,
-Ask the doctor or nurse to wash his hands
-Ask whether stethoscopes were cleaned between patients
-Ask whether the pen being used is specific to your room, if not, request or provide a pen for use in your room only.
-Leave as soon as you are reasonably able.

Would anyone like to suggest anything else or come up with a snazzy acronym for all of this? The safety of all videojug viewers may depend on this production!

Grateful

2010-11-25T23:27:00.000-08:00

The students at UC Merced are a unique cohort. More than 90% of them are first generation college students. They have no sense of entitlement and they roll with the punches. If a classroom gets changed, they all show up in the new room without batting an eyelid. If the curriculum for their major changes, they find out what they need to do and they just do it. They don't make up excuses for themselves. This doesn't mean that they all get perfect grades, but they don't blame their bad grades on anyone besides themselves.

I have a very soft spot for the students. There are some among their ranks who are as smart and hardworking as anyone I have ever met, but they have no idea of their potential or the opportunities available to them. They show up thinking that a college education means becoming a teacher, doctor, dentist, or lawyer because those are the only four types of educated professionals they have met. They think that one of those jobs is better than agricultural work or factory work, so they come.

I see a bit of myself in those students. I had it better than they did. My dad is an engineer and my mom emphasized education. They sent me to a private school from kindergarten through the third grade. The school building was an old church and when the student body assembled, we all sat under a stained glass window that contained the words "The glory of God is intelligence". I was raised to believe that. But a lot of the time, I didn't know what was going on in school. I figured if I just studied and got good grades it would be enough. I missed a lot of opportunities, so I am sympathetic to the students who are studying, getting good grades, but a little clueless about what else they should do to get accepted to medical school, or some other professional program. That is why I have more undergrads working in my lab than I really need, and why I meet with each of them each week. We talk about research, but we also talk about career paths, opportunities, and how to get where they want to go in life. For the first time in many of their lives, someone takes them seriously.

Last week, I was lecturing about genetics and heritability. The text focuses heavily on the heritability of IQ, which is a contentious topic. The studies in the textbook were flawed. The authors showed that 42% of IQ is determined by parental effects and they went on to say that meant genetic effects. I explained to them that while parents give us our genes, they also have a strong influence on the environment their children grow up in. From pre-natal vitamins and breastfeeding, to reading bedtime stories, parents shape the early environment of their children.

I told them about my genius nieces and nephews, but they are descended from smart parents; their mom teaches them to read and and do arithmetic when they are little, and their dad does science experiments with them on the weekends. Many of the students looked at me with a bit of jealousy and longing. I could see in many faces the desire for moms and dad with the knowledge necessary to help them with homework, and the time to spend teaching their children. In that moment, I understood what a huge leap it has been for my students to even make it to a university and how determined and strong they really are. I understood that they have it in them to change society and technology. I am certain that some will. For many though, since they are the first in their families to even see those possibilities, they may miss the opportunity to directly contribute to anything that seems to have global importance. However, I think those students will read to their children, help with homework, and help their children find and take advantage of every available opportunity. As they share what they learn with those who come after them, they may change the future of society in greater ways than anyone might fathom.

Prizes for procrastination

2010-11-23T21:22:00.000-08:00

I am required by the state of California to periodically take sexual harassment training courses. I hate doing it. As the student/professor relationship is sacrosanct to me, I would never consider making sexual advances on a student or harassing a student. Also, I don't worry too much about harassing my co-workers. The reason for that is simple. I have always been the one blushing when humor starts to head south and I generally avoid topics that bring out my crimson.

I have had bigger things on my mind these days than sexual harassment training. The training takes two hours and it is mind-numbing. And honestly, what will they(?) do if I don't take it? Make me stop teaching? Doubtful.

I was supposed to complete it a while ago, but my plan has been to complete it over Christmas break when there is less going on. Apparently that wasn't good enough. I received notice that the university is preparing a live theatre version of the training for those of us who have not yet completed it. It is scheduled on Dec 14th. I am signed up for it. If it is anything like the animations in the online version, there will be groping, off-colored humor, and sexually suggestive material. I have no idea who the actors will be. If they are any of the local "stars" it will be awkward and amateurish. Overall, I anticipate a rather uncomfortable, and funny in the wrong way sort of production. I will do well to refrain from laughing in all the wrong places. If it is bad enough, maybe I will even file a sexual harassment complaint at the end.

Hide and Seek

2010-11-22T21:15:00.000-08:00

My house is cold. The thermostat says 55º (12.8º C). The obvious reason for that temperature is that I haven't turned on the heat. Now at this exact moment, I can imagine my mom's foot tapping and her saying in the accompanying voice, "TURN-ON-THE-HEAT. This is why you get a job!...so you can heat your house." And well.....that response is warranted. I made a vow after leaving Rochester, NY to never again pay $300 a month to keep a house at 55º. What I meant was that I never wanted to live somewhere that cold again in an uninsulated house. So I live somewhere warmer in an uninsulated house and energy costs are still really high and I hate turning the heat on. I will insulate my house when I overcome my fear of the crawl space and attic, which hasn't happened yet so sometimes I let my house get cold to assuage my guilt about living in an uninsulated house. This time though, I have a legitimate excuse. And I can now imagine my mom grumbling in a very dubious tone "Uh sure. Okay, let's hear it."

So here it is. I got my face lasered.

Lasers are remarkable things. They emit really intense light at a specific wavelength. Exactly one color is present in laser light. Whatever absorbs that color of light gets burned and whatever doesn't is untouched. I went in for some green and yellow laser light which means that it was absorbed by blood. There was enough energy absorbed by the blood to heat up the capillaries through which the blood flowed and burn them too.

When I told my nieces I was going to get my face zapped by lasers, they looked horrified and asked "Why would you want to do that?" Any adult who knows me well, instantly knows the answer. My face is (wait, was!) really red and it would turn the color of a tomato at the least hint of emotion. A lot of emotion would turn my face purple. On more than one occasion, people have expected me to collapse from a heart attack.

Honestly, I did my best to rein in the color. I learned to not get upset in the moment, to not get embarrassed at anything, to lower my pulse by breathing slowly..... to generally keep all emotions in check. But, I'm human. And so when I would get flustered, I would turn really red and everyone would get out of my way because they thought I was really mad, but I wasn't. When people would talk to me and I was trying to remember their names, I would turn red and they would think they had embarrassed me, or that I didn't like them and they would politely leave me to myself. And once when I was trying on some hideous sandal boot things to humor my sister, I got the whole store laughing. It wasn't because of the boots, it was the color of my face once I started laughing. In general, people always overreact to my emotions because my face is (I mean was) overreacting first.

I used to be really shy because of how red my face would turn. Barry worked with me through that. He told me it wasn't that bad and it didn't matter as long as I didn't let it stop me. He took me at my word too. I told him it meant nothing when my face went red and he believed me. If I was crying or shouting, he would infer that I was upset, but up to that point, he always assumed my emotions were in the neutral/calm zone. It was nice to be around someone who didn't overreact.

Tom always treated me normally too, and he also understands a bit more than Barry. Tom is my brother and he looks like my brother. We share some physical similarities. However, the most similar part of us is our mental processes. This is hard to explain, because it isn't just a feature, it is sort of who we are. I can predict what Tom will do better than he can, and he can predict how I will feel better than I can. We trust each other a lot. So when I call Tom and say "I am thinking about getting some eggs frozen down." and he says "Maybe you should get your face lasered instead.", I take him seriously.

As a consequence, my face is less red than it used to be although it is still a little swollen and red from inflammation. After all, it was burned, or at least the blood vessel part of it. The cold air in my house helps the inflammation to go down and it doesn't hurt as much.

When I was at school today, I told Maria. She said she was going to sneak up on me and tickle me. The thought of that made me nervous and I felt my stomach tighten, but very little color went to my cheeks. She was impressed. I told Matt. He was just disappointed. His favorite hobby is banging on my office door really loudly to see how high he can make me jump and how red he can make me turn. I think he'll get over it.

I think Tom knew what would happen, but I was honestly surprised. I was looking in a mirror trying to make myself blush. I could think of lots of embarrassing things and they didn't make me blush. And I thought of happy things and sad things and angry things and my face stayed the same color. And I felt a lot of very personal emotions and they didn't show at all. Suddenly the bands reining in my tightly controlled emotions burst and my honest true feelings about everything came closer to the surface. I think I am going to let them stay there from now on. I think that now they can be hidden from everyone else, there is no reason to hide them from me.

One of the perks of working at UC Merced

2010-11-18T13:33:00.000-08:00

Persimmon season!

(Psss! Maria, they are in the front office.)

I am happier that I pay taxes when I see stuff like this

2010-11-16T08:39:00.000-08:00

There are some seriously warped people at CDC. That is why they are so cool.
Check out these videos. They also have some new Health e-cards that are surprisingly annoying and funny.

verbing weirds language

2010-11-15T19:28:00.000-08:00

I love how the English language changes so quickly. I love the Urban Dictionary because it keeps me hip (or it would if I ever had been). Words like "ridonkulous", "refudiate", and "sawesome" are simply delightful. My sisters are more abreast of the cutting edge of pop-culture than I could ever hope to be, and they pull out fun facts about new words on a regular basis. One sister, Marie, is an English teacher, and the other, Laura, a student in graphic design. Both of their disciplines have an appreciation for nouveaux mots. There are times I would love to be as cool as they are and incorporate words at the cutting edge of the English into scientific writing.

Right now, I am writing a manuscript about additivity and adaptive landscapes. It is an intimidating field to enter, because scientists of extremely high caliber dominate that area of research and I am a new comer. I have absolute confidence in the math as I work with Kristina Crona, an extremely high caliber mathematician; she does all of the worrying about that. She is incredibly fluent in math and she makes it seem very accessible. I am responsible for the English language portion of the manuscript and so I do all of the worrying about that. Sometimes I get tired of trying to be correct and I just want to blow people away with my mad language skills. It feels pretty sawesome to refudiate the approaches others have taken and I would love to express our results in exactly those terms, but that would seem ridonkulous. So I stick to the good old OED and follow a more conservative path.

It nearly kills me though. We were lacking the verb we needed and the word "error" would have been perfect, except that it's a noun. ("Err" just didn't sound right.) Kristina, a Swedish woman, has caught on to the evolvability of English and suggested we just go ahead and use "error". I would have loved to give it a try, but I doubt the Urban Dictionary pulls words from scientific articles, so we wouldn't have even had their backing.

Happy, Happy Veterans Day

2010-11-11T09:24:00.000-08:00

At this exact moment, I am caught up with writing. This does not mean I am anywhere close to done. There are several people who could hit "send" at any moment and make it so I am not caught up any more. And, honestly, there is writing I could do in a responsible and proactive sort of way to actually get a bit ahead, but I think I will not spend today that way.

My sisters are coming(!) and I want to get ready for them. Okay, it is really more than just getting ready for them, it is also rising above my current status of THE ghetto neighbor since I haven't mowed the lawn in about three weeks. I haven't exercised for 3 weeks either and so maybe I will do that too.

The neighbor kids just stopped by asking if I needed them to do my yard. I happily told them "No, I'm on it today." So I had better go and get on with it. I hope everyone has as happy a day as I will. : )

James!

2010-11-08T15:01:00.000-08:00

I didn't convince him to go back to school. He did that on his own. But after years of encouraging him to do so, I was the first one he called for advice about registering for classes. He is going to major in psychology.

Way to go bro! You'll do great!

Videojug conundrum

2010-11-07T20:51:00.000-08:00

Videojug:
The VideoJug Philosophy

I got asked by an editor at videojug to make a video about microbes or antibiotic resistance for their website. I love videojug. It is hilarious and useful. I learned about writing business plans, marketing, magic tricks, repairing t-shirts and making an old couch look new on that website. I have had more than a few laughs and I have entertained my nieces with it. They have videos about how to do nearly everything. And they want little old me to make a video for them.

Of course I will do it. Of course! But now comes the hard part. What should I tell people how to do? I can submit more than one video. But what do people want to know about?

My first thought was to make a video about how to do at home stool replacement therapy. One of the readers of my blog had a Clostridium difficile infection, thought she might die (really), and emailed me for months about her efforts to get better from it. She is a friend at this point. After being denied stool replacement therapy by all available medical centers, she finally did it at home and she is better now. There is a need for that information to get out. However, I am not actually an expert in that....and there might be to great of a liability associated with that.

So then I turn to the things I am good at....and I don't know if anyone wants to know about them.
How to make a phylogeny....a little boring.
How to make cleaning the fridge fun by identifying the microbes growing in it!.....overly optimistic.
How to see if MRSA has colonized your nasal cavity.....not relevant for most people.

I am thinking that maybe I could show how to do some great science projects for K-12 students, but I am curious if anyone out there has any requests....If you read this blog, then maybe there is something you would like to know about microbes.

If so, what?

O Fortuna!

2010-11-06T10:35:00.000-07:00

I have been logging one grant application per week for about a month now. I write and I sleep and I teach, when necessary. The senior faculty all told me that waiting an additional year to go for tenure would give me more time to write and get grants, and I guess that it does....about three months. Most grants take several months to go through the review process, so if the funds are to be made available before the June 30 deadline for tenure next year, they need to be written now, or a couple of weeks ago. To be fair, some of the proposal deadlines were added to my calendar before the whole your-grant-would-not-get-you-tenure-at-Berkeley shake-up.

The proposals are exciting and they are all different: Melting bacteria to identify species, measuring the thermal output of bacteria, metagenomics of the microbiota in the human gut, and developing new mathematical approaches for analyzing adaptive landscapes using the evolution of antibiotic resistance as a model. There are a couple other proposals I am working on too, but I can't talk about them yet. I am the lead investigator on roughly half of the proposals, and all of them have required a substantial amount of time and work, which is why I write, sleep, and teach when necessary.

Back when all of the senior faculty thought I was a shoe-in for tenure, I added things to my schedule besides writing grants. I decided to fullfill my teaching load for the entire year this semester so that I could spend a lot of time advising my two new graduate students next semester. I bought season passes to the San Francisco Symphony. Both of those choices seemed to make sense when I made them, but now, with so much to do is so little time, those decisions seem reckless, poorly planned, and I often wonder how I will make time for them. If I could go back in time, perhaps I would make choices that could make those commitments go away.

Unfortunately, the teaching hasn't gone away, but then neither have the season passes. I went to my first symphony of the season last night, with a friend. The symphony was Carmina Burana and the opening notes of it were like a thunder storm breaking in the desert and a subsequent flash flood that sweeps away the dust, dried out wood, and debris that has accumulated. And then the thrilling percussion sprinkled into the music here and there were like drops of rain coming much more slowly, the kind of rain that has time to penetrate, hydrate, and allow life to go on. The chorus of children singing high and clear reaffirmed that life continues, and is good.

Next weekend, the symphony will be Rufus Wainwright, singing five Shakespearean sonnets and I will go with my sisters. Then I will be off from the symphony until February. I think that those two concerts might pour enough life into me to get me by until then.

Proof that I wear heels

2010-11-05T12:24:00.000-07:00

Take that Cesar! Hah!

Oh Brother!

2010-11-03T15:45:00.000-07:00

Tom called me last week to let me know he had collected a bacterial isolate that reminded him of me. I thought it was sweet (sort of). The strain was resistant to almost all of the beta-lactam antibiotics tested against it, and when I told him which genes it was probably expressing, he broke from our conversation briefly to tell a colleague what my response was. He sounded like he thought I was cool as he was talking about me.

One of the great things about a large family is all of the great people I have gotten to know really well throughout my life. Tom is certainly included in that camp. He is two years younger than me and we were often partners in crime while growing up, except that under Tom's influence, the "crimes" were usually acts of service. Pushing people out of snow drifts on days when no one should be on the roads, hiding a grandfather clock for four months to give our mom for Christmas (She wasn't fooled. She knew what we were up to the whole time.), stuff like that.

Tom is strange, because with him, gender roles make absolute sense. When we used to go camping, he chopped the wood and I built the fire and cooked the meal. Tom was perfectly willing to let me chop rather than cook. He even taught me how, but I honestly hate chopping wood and I am bad at it. I will gladly cook on any day that wood needs chopping. When Tom used to fix cars in high school and college, I sometimes brought him sandwiches. No problem. He bought a lot of the gasoline that got us around. I could bring him lunch or dinner.

Tom has four children now and a really cool wife, and he lets me be an influential aunt. The children like me to teach them science and how to do cool things with paper. Perhaps his two oldest will work in my lab a bit this summer. However, he doesn't always appreciate my influence. He has sworn revenge on me for sponsoring screaming contests. If I ever have children of my own, I am toast.

Now that we are mostly grown up, Tom and I still have fun together, (we will go to a U of U football game in San Diego in a few weeks.) but now we have a semi-professional relationship too. He is a dermatologist in the Navy and has a doctorate in health education. He writes papers, I write papers, and we read each others writing. We have one on-going collaboration that involves melting bacteria (don't ask, not yet anyway) and it looks like we may finally get a Barlow & Barlow publication in the spring sometime. I give him updates on my patents and he gives me updates on his progress. He usually initiates these discussions over the phone in the last three hours of a long drive when I am going from one place to another.

Tom is one of the busiest men I know, still doing random acts of service, being the best dad/husband/doctor he can be, and who knows what else. And so when he calls to tell me that something as insignificant as a bacterial isolate is making him think of me, my heart melts.

Election Day

2010-11-02T17:53:00.000-07:00

I am back in the land of the living, almost. After 15 hours flat on my back with some illness, probably viral, I can get up and move around some. I forced myself to get up and give a genetics lecture today and that was probably a good choice, probably......but I am struggling to make myself go vote.

I think I was saturated with politics by the age of seven. My dad used to haul me and my many siblings out in the station wagon to deliver political leaflets to doorsteps of houses. He took us to political conventions, and he indoctrinated us with his political views. Mostly I agree with my dad, except that I don't care nearly as much as he does.

I have passion about many things, even ridiculous things. Like composting, recycling, avoiding cruelty to animals including insects, planting my own garden, and using things until they fall apart. And I probably learned all of them from my dad, but somehow the political fervor just didn't quite make the leap.

Sometimes I think about not getting out to vote, but then I remember one occasion, when I was six. I had been delivering political leaflets all day and I was bored and tired and wanted to go home, but the stacks still hadn't run out. It seemed like they never would. I pulled out my dads electrical shaver and started dissecting it and in the course of doing so, I discovered the trimmer on the top. I asked what it was for. My dad told me it could be used to trim sideburns and so I asked if I could trim his. He was reluctant, but I begged and he finally told me I could trim them just a little. Well of course, it was more powerful than I thought it would be and I was only six. Of course my hand slipped and the whole sideburn was gone. My dad sighed and squinted a little when he looked at it and then he let me trim the other to match (which it did in the end). And he just laughed.

Somehow when I think of that, politics make a bit more sense. And I think I will make myself move from the sofa and go vote.

Blogging for a cause

2010-11-02T04:58:00.000-07:00

Awkward

2010-10-28T10:14:00.000-07:00

I finally taught a lecture about sexually transmitted infections yesterday. I have found good reason for not doing so in all the classes I have taught so far. However, in a course entitled "The molecular basis of human disease", it seemed like an important topic to cover. Perhaps if I studied cancer or heart disease, I could derail the class into one of those topics for countless lectures and justify my doing so by their importance. But I study bacteria, and I have been on the thesis committees of seemingly countless students studying chlamydia, so this is a much more natural topic for me to get hung up on, except for the awkwardness of it. I am always scared of the questions people might ask. In response to my blog, I get some strange, (albeit serious) questions about sexual issues. Often they make my face turn red, and my response is a muttered "You do what?! and why????" Not good turf to tread on in a lecture.....

That said, I let the kids in my class ask about all sorts of things. It is a course for non-majors and some of them have misconceptions about biology that are well beyond anything I could anticipate. The 76 students are all pretty friendly, and so (I think) they feel safe safe in class and they are excited about learning. When they saw the first lecture slide yesterday, they all started staring at the ground. It was just a title slide, but I think they foresaw the obligatory pictures of genital warts and the like that were coming. So I tried to lighten things up with a funny story. We started by discussing transmission of diseases and I told them about how in high school and OB/GYN came to human biology to teach us similar material. When he asked us what the warm, wet places were where one could catch STIs were, one kid raised his hand and said "Armpits?"

That got the class smiling at least and they could bear to look up, so I kept the funny stories rolling. I told the one about a doctor who congratulated a friend for getting scabies, because it can be considered an STI, and another about a very loud ménage a trois in a hotel room next to mine and the diseases I wished on them. The students all gagged when the obligatory genital wart pictures came up, but overall they seemed to be having as enjoyable of a time as possible. The atmosphere was comfortable, maybe too much so, because then a student asked a question that I had never fathomed. "So what do you think about the theory that the Mormons created HIV to kill off the people who don't believe in God?"

A strand of thoughts lit off like firecrackers exploding in my head as I considered the number of problems with that question.
Does he know who he's talking to?Does he really believe that? Do I address the science part of the question or the religion part of the question? There is so much wrong with that question.
Then reason kicked back in.
How do I answer without shutting down the class and making them shy to ever ask questions again?

I decided to focus on the epidemiology of HIV and explained how in the early years it was spread in some parts of Africa by the re-use of needles in health care clinics. I told him there had been sloppiness, laziness, and a lack of education, and that some people thought it was a conspiracy to spread HIV that way, but I knew of nothing to suggest so. I talked about some of the health problems in Africa and how some people in official capacities had seemed callous towards the African continent when the whole problem was getting going. That seemed to upset some of the black students and so I focused on technologies of the time and tried to lighten things up with some strange reports of Soviet bio-weapons and whether it was even technologically possible to make HIV. Some of the students started looking at me like I was insane. By the end of my answer I was feeling really awkward and many of the students were starring at the floor again. Awkward.

I was really relieved when we finally got to the end of lecture because it was done. And I must admit that I was a little relieved to know that there are topics MUCH more awkward to discuss than the transmission of STIs. In a matter of 5 minutes, I seemed to have found them all.

Note to self:
Avoid lecture topics of religion, injustices to Africa, conspiracy theories and rumored reports of Cold-War arms races. Never tread on that turf again.

Corrupting the universe one student at a time

2010-10-20T10:27:00.000-07:00

When Francisco Ayala interviewed me for the job I now have, the first question he asked me was about adaptive mutagenesis. I have never studied adaptive mutagenesis, nor do I plan to. I have never written about it, spoken about it, or even spent much time looking at the data. It is a very contentious area of research centered around the occurrence of seemingly non-random mutations in non-dividing cells. My thesis advisor, Barry Hall forbade me from even thinking about it and he refused to teach me about it even though, at the time, he was one of the leading researchers in the field. He cared about me, saw I had iconoclastic tendencies and wanted to steer me clear of a whole heap of trouble. As usual, he was right. For the first year or so of my independent career, I got asked more about adaptive mutagenesis than my own research. (Barry is always right.) During my job interview, after explaining that I had never touched the topic of adaptive mutagenesis in any way, Francisco then asked about whether I would teach it to my students. I wouldn't. Then I heard about the responsibility of teachers and how irresponsible it would be to teach adaptive mutagenesis to them. I promised. We then discussed my work.

When Tony Dean found out that I am the genetics teacher at UC Merced, he exclaimed "Oh good heavens! What were they thinking? You'll corrupt generations of students!" I told him about my interview and told him that I stick very closely to the text book and that I am responsible and prepare the students for the MCAT. He smiled at me and said "I wouldn't be nearly so responsible if I was in your position...."

Barry is always right, but Tony is too, just in a different sort of way. If Barry is a father-figure, Tony is a mischievous older cousin. And he got me thinking. Not so much about adaptive mutagenesis, but my own research. I have published all sorts of controversial findings about recombination in bacteria, and that antibiotics haven't changed bacteria in the ways we think, and that antibiotics have changed bacteria in ways we didn't think they would, and that prescribing amoxicillin to everyone a lot might fix the antibiotic resistance problem.

I started teaching this stuff to my students. They love it. I tell them that this is my own view of bacteria, but I explain the genetics of it and it makes sense to them. I have totally accepted the responsibility of corrupting those students with my views. Why not? They may as well get something unique out of their education. But maybe it turns out that my approach isn't as unique as I thought. Last week Ellen Simms emailed me and told me she taught her students at Berkeley about my research and they loved it. And then Joe Alcock flew me down to Albuquerque to teach his students my views on bacteria, and they liked it enough to stay awake for the 2 hr 15 min lecture I gave in the evening, and then they come for sushi after. (OK, the sushi was probably the real draw of going out for sushi, but we had good discussions.)

There are a lot of students that I am corrupting and I like that, and maybe I am beginning to feel like it isn't complete corruption. I do wonder a bit though if I can still feel like an iconoclast if my ideas go mainstream. I won't lose any sleep over that question though.

Non-olfactory Grant money

2010-10-16T15:16:00.000-07:00

There is a cockroach trapped under a bucket of plaster in my living room. It has been under there for three days. It is the sort that abounds outside and so I hope it is just one that snuck in. I am scared of lifting the plaster bucket and losing the roach, so I may just leave it there until it is dead. The cruelty of that decision is regrettable, but I just don't want to deal with it right now.

People keep picking at me for information that isn't mine to give. They want to know about my brother's recent announcement that he is gay, about my family, about my feelings. Mostly, none of this is mine to talk about, and the small part that is, isn't anything I want to talk about. I love my brother the same as before. I don't know what else anyone needs to know. It seems like love that strong is enough. I don't think that I have to open up and let every facet of my emotions out for everyone to see. Perhaps my withdrawing is cruel. Perhaps there is comfort to be found in collective responses but right now, it just seems like gossip and I don't want to deal with that.

I got an R15 grant from the NIH. Combined with the peer-reviewed publications I've had in the last five years, everyone at my institution thought that I was a strong candidate for tenure, but they felt we didn't have the expertise necessary to review my case within the school. They sent it out to two anonymous committee members at other Universities who responded to it saying that they wouldn't tenure someone at their institutions who had an R-15 grant. They are absolutely correct about that. Their institutions wouldn't qualify for an R-15 grant because it is money earmarked for small research institutions that receive very little money. However, they also expressed the sentiment that the money was less good than money from other grants. The amount was fine, and sufficient for sustaining my research, but the source wasn't good enough.

My senior colleagues went into frantic action, just like at a dinner party when a mouse suddenly runs across the floor. Everyone was talking nervously about me and trying to decide what to do. Some of them ran but many wanted to meet with me and hear what I had to say. Rules were made, meetings were held, and still no one at my institution can decide whether my grant is good enough or not. So I have delayed applying for tenure for one year. When I go up next year, I will be reviewed by clinical microbiologists instead of evolutionary biologists and perhaps I will have other, more respectable grants. My career gets to incubate a little while longer and then we will see.

Delightful intelligence

2010-08-30T11:23:00.000-07:00

My lab group is growing and I adore the people joining me. They are all tremendously intelligent. Once, I attended a talk where an incredibly successful scientist (whose name I have forgotten) told us that the secret to success was to work with people more intelligent than we were. My heart sank when he said that because there was no way of deluding myself that anyone in my group was smarter than me. My staff scientist had just left, the undergrads were enthusiastic but not particularly useful and my graduate student was just giving up and about to leave the program. However, I set a goal to only bring people into my lab who were more intelligent than me after that.

That goal is finally coming to fruition. I have one fabulous graduate student (Christiane Guillart) with another soon to join (Lolo Cardenas), an excellent technician (Anna Nandipati), and some really bright undergrads. I feel like my lab is starting to radiate with intelligence and creativity. Not only do these people bring creative ideas, they are sounding boards for my own. Science is becoming more fun and I find myself working longer hours in the lab. We have a grant and a fun project to do. It doesn't get much better.

Little changes

2010-07-22T11:50:00.000-07:00

I should be blogging about the new gel that reduces the transmission of HIV to women by 35%. It will save millions of lives and empower women who have little to no control in matters of sex. That is what I had meant to blog about today.

However, it turns out that there is a spontaneous celebration going on in my lab right now over site-directed mutagenesis. In theory, SDM is one of the easiest things to accomplish in the lab. As a grad student and post-doc, I never had any problems with it. It just worked. On the worst days, at least half of the colonies I screened would have the mutation I had meant to introduce by SDM.

And then I started working at UC Merced and SDM stopped working in my lab.

Now I can handle the toilets not flushing properly on the third floor, and I can handle the leak in the ceiling above my lab that keeps springing up. I can handle construction workers setting off the fire alarms, resulting in a lengthy evacuation of the building when I am paying a repairman by the hour to fix my equipment, but it has been really hard to handle SDM not working.

Okay, it didn't stop working entirely. That would have shut down my lab. I had a Polish research scientist in my lab for a while who could make SDM work by some arcane method that involved way too many steps that no one else could get to work. I had a graduate student who was able to introduce some mutations by sheer stubbornness and numerous attempts, most of which failed. However, the days when SDM just worked and was a reliable and quick way of designing a restriction site, or introducing a silent mutation for some assay were over. We only used SDM to change protein sequence when it was absolutely necessary. Research wasn't stopped, but it was seriously slowed down.

Then today SDM started working again in my lab. After five years of beating my head against it, it just worked. I mean really worked, the way it's supposed to. 100% of the colonies we sequenced had the mutation we wanted.

I might make it as a scientist yet.

Life like a Desert

2010-07-09T17:01:00.000-07:00

I am always amazed by the desert. It changes. Places I have been hundreds of times always seem different. Maybe it's the light, hitting off the colored rocks and cliffs. Places that were darkened by shadows that then look completely different when fully exposed. Clouds spread across the sky, sometimes still and calm, or else furiously blowing over and their shadows flickering by like a the cars of a train, the wind shaking and blowing the car, or tent or wherever shelter has been found. And then water in so many forms. Cylinders of rain pouring down, sometimes over the freeway. Perfect visibility on the outside, and then suddenly way too close to see anything but darkness. The sound of water pouring down like THE END is coming, whatever end that may be... an oncoming semi, armageddon, possibly worse, and only the approximate knowledge of how big that tempestuous cylinder was from the outside makes it seem possible to keep going. Then on the other side, blue sky again, so suddenly and vibrant purple water left from where that cylinder of doom made it's rounds. The sun shining down brightly and beautifully like nothing was ever wrong.

Solid Success

2010-06-29T20:05:00.000-07:00

I think that it is good when success comes slowly and in small doses. It is more lasting that way. When it is so hard fought that it isn't ephemeral and can't even be ephemeral. Mountains were moved and millions of individual blades of grass planted to make it happen. That is when success is sweetest.

That's how success comes to me anyway. I can't win a game of bingo. Slot machines have the return rate of storm drains when I play them, (which I don't for obvious reasons). For me, success isn't easy. At various points in my life, being healthy has required walking slowly 20 minutes a day as physical therapy so that I could walk at all. Or giving up gluten and having to start over and develop a new diet from scratch. Those efforts weren't fun, but in the process, I think I have come to know my body really well. The things it needs and the things that harm it.

I don't think that successes like that only work at a personal level. I think success also works like that at a societal level. I have been hanging out at various county public health clinics these days. I am getting bunches of shots to protect me from exotic diseases like typhoid and yellow fever and more common diseases like hepatitis A and B. Parasitologists sort of brag about all the parasites they catch in the field, but it isn't really like that for microbiologists. Our organisms are just too deadly.

I sort of like hanging out in public health clinics. I think they are sort of a fulfillment of the "American Dream"or maybe just the dream of living in developed nations. People from every ethnicity around are there seeking better health for themselves and their children. There are translators with all sorts of exotic language skills to help every person who needs assistance. It doesn't matter that there are low ceilings, flickering fluorescent lightbulbs, and dingy industrial strength plastic chairs. One person at a time gets treated like an individual and a human and gets vaccinated. One person at a time is protected from many of the most miserable pathogens alive. And despite the humble appearance of those clinics, phenomenal technologies have been developed to so that public health can be administered efficiently and safely.

It is wonderful that so few people in America actually know what diphtheria is. And wonderful that the polio vaccine is no longer required in most countries. The success of public health is strong when it is successful. Public health is most successful when no one gets sick.

Right now, despite the sweeping health reform package that passed, public health has almost no funding. Not in California anyway, which is one of the places it is needed worst since there are so many immigrants from countries without functioning public health programs. It has surprised me to find that out since so much money has been earmarked for healthcare. I thought we were supposed to be building a healthier nation, and vaccinations, exercise, eating vegetables, and breast feeding children are some of the most effective and least expensive ways of improving health. But the money that promotes those causes is evaporating as the first thing to go when budget cuts are required.

The same thing happened when the first George Bush was in office. I still remember the protestors chants on TV. "Twenty million died from AIDS. Where was George?" He found the funding to pay for AIDS research in the scant coffers of the tuberculosis management program. All of the money spent on tracking, calling, and forcing (when necessary) TB patients to take their medications was siphoned off into HIV research. Now, most AIDS patients die from TB because it was neglected, but the money for public health hasn't returned. It just gets more scarce.

Thankfully, public health in America is still pretty good. Most people don't get mumps, measles, rubella, diphtheria, tetanus, or pertussis. HCV vaccinations are given to young women to keep them safe. Technological mountains have been moved and millions of individuals immunized or treated one at a time to make it that way. But even mountains can erode away. The pubic health nurses I have talked to lately say that hepatitis A and measles are causing a lot of problems right now, because not so many people are getting vaccinated. Obesity, protected sex, and breast feeding campaigns suffer even more in the wake of budget cuts.

A lot of money has been earmarked for healthcare, and I don't think that all of it has a clear destination. I hope that some of it ends up going into public health efforts, which is one of the most efficient ways it could be spent.

Hooray!!!!!

2010-06-20T15:36:00.000-07:00

I just got word that my first NIH grant will be funded. This means I am eligible for tenure. Hooray!

Summer Reading

2010-06-19T22:59:00.000-07:00

Without a doubt, the short story is my favorite form of literature. The first book that was ever given to me as a gift was Just So Stories by Rudyard Kipling and I read it until it fell apart and I kept reading it and still do sometimes. Then I read the Grimm fairy tales (the real ones), and different mythologies and Gypsy stories and every other short story I could lay hands on.

For me, the main appeal is that the density of important details is very high. In relatively few pages, some sort of conflict is laid out and then addressed. Often, little details can be brought together in unexpected ways to make something fascinating from the mundane (think of Sherlock Holmes, for example). In a short story, it is done so quickly, that it is like watching a magician perform. It's hard to figure out how it works. Which is also the problem with short stories.

Against all wisdom, I took the creative writing courses in college instead of technical writing. They were great. I loved my poetry class and I was so excited to have a class on short stories...until I stared reading the assigned readings. Those stories were all about postmodern people and postmodern relationships. Yep, all of them. I am sitting here ticking them off. There was one about a girl wanting her boyfriend to put on a full body latex condom before making love. And another about a food critic who only liked fugu because it made her mouth numb. And some other about a girl who wanted to dump her long standing boyfriend for a guy in a photo who she thought was her soul mate. I vaguely remember one about a guy in super hero clothes who was trying to define himself by riding around under semi trucks. (I sort of liked that one except there were too many descriptions of vomit.).....And then we started workshopping each others stories in class and they were mostly about bad sex and dead babies. I really started wishing that people (not me, but somebody) still worshipped Greek or Egyptian gods so that we could get some new myths.

I think that's part of why I became a scientist. A good article reads a bit like a short story and has a high density of information. Okay, so maybe there is some technical information to wade through, but if that doesn't induce a comatose state, then the actual story told by the experiments can be quite engaging. Somehow though, even a good article just doesn't quite satisfy the same craving as a good story. I think it's because when the author tries to draw together a bunch of little details into some magnificent conclusion the editor calls it wild speculation and sends it back for revision. (I used to try to argue with the editors over it. I don't anymore. I blog instead.)

Lately though, I have been having some good luck finding good short stories. That's mostly what I have been reading this summer. They sort of fit in nicely between things and I can read one in the evening after I'm done in the lab, or on Saturday after weeding a flower bed and before mowing the lawn. On the off chance that the readers of my blog like a good short story, here are some of the places I have been finding them.

The New Yorker: I find myself annoyed with some of the news articles, but I have found some good short stories in there. Joyce Carol Oats and Allegra Goodman are great.

Sherlock Holmes: There are zillions of Sherlock Holmes stories and some are better than others. I have been pleasantly surprised how by their variety however, and I have been able to read more than I thought I would without getting sick of them.

Stories: It's an anthology of short stories edited by Neil Gaiman and Al Sarrantonio. They are dark and I sort of feel like a kid reading the Grimm Fairy Tales again, except there are many authors and more variety.

Tengo pasion, nada mas!

2010-06-07T21:33:00.000-07:00

I think that at the heart of many nerds lies a desire for games like Dungeons and Dragons. I have never played D&D, so I can't be sure, but I once watched my cousin play it and I kind of got the gist of it. It is all about strategies and a little bit of luck. All sorts of virtual battles are waged and the thrill comes much more from the battle itself than the actual winning or losing of it.

I have a little bit of that sort of nerd in me. Instead of D&D, my friends and I used to come up with strategies, on paper, for launching bioterrorism campaigns against the USA. It started out as an academic exercise. We all worked in infection control and we kept honing our ideas of what the nation should prepare for. At some point though (probably around the time we had come up with a hypothetical hit-list of the people who were most capable of responding to bioterrorism attacks) we decided that our little thought experiments were getting a little too good and a little bit out of hand and we stopped. (Please note: this was many years ago and our ideas are quite out of date, which is the only reason I am willing to even blog about this.) Though we had done nothing wrong, we abandoned those evil ideas and devoted our sciences entirely to the betterment of humanity.

One of my ways of bettering humanity is fighting heart and soul against antibiotic resistance. I worry over it, sleep, on it, work on it, strategize how to combat it and sometimes blog about it. It is more satisfying than a mere game, because I actually get to test the ideas I have. I get to go in the lab and kill bacteria and then try to figure out how they will figure out how to live. I love it, but it sometimes feels a bit lonely and pointless. Sometimes close friends and colleagues lose a family member and they blame it on the cancer or the heart problem, but it was really the antibiotic resistant infections they developed during their treatments that took them. Such instances hurt because I feel that I have failed those I care for by not finding a solution fast enough, and because those close to me, despite hearing about antibiotic resistance more than they would ever want, don't realize that antibiotic resistant bacteria are what took their loved one. When the government chooses to fund studies of bioterrorism over studies of antibiotic resistance, it also feels a little lonely and pointless.

Lately though, I have come across a bunch of people as passionate about the problem as I am.

The Pew Charitable Trusts are working furiously to save antibiotics by restricting the use of some of them in farm animals. The very sound idea backing up their measures is that if we stop using many antibiotic is agricultural environments, they will last longer in clinical environments. They have a great website summarizing their efforts and a lot of other information. As a researcher of antibiotic resistance in one of the biggest agricultural regions in the US, they have asked me to work with them a bit and I am excited about doing that.

Kimberly-Clark has launched an effort called "Not on my Watch" to prevent the spread of of Healthcare associated infections. They have compiled numerous resources and organized numerous events to help provide health-care workers with the knowledge necessary to keep patients safe from the deadly pathogens lurking inside hospitals. They are quite passionate about eliminating infections that occur in hospitals and other health-care facilities.

BioShield Technologies is a company that sells products to prevent the occurrence of resistance. They use silver that has been sequestered inside of porous ceramic particles. When those tiny ceramic particles come in contact with bacteria, the silver is drawn out and it kills the bacteria. Although bacteria can become somewhat resistant to silver, it is a lot harder than for antibiotics and the mechanisms are not effective at high concentrations. Bioshield incorporates those particles into an epoxy coating that can be painted on to surfaces in health care environments. They also sell products like cuffs, stethoscope diaphragms, pens and clipboards that have silver built into the polymer that they are made from. By killing bacteria on the surfaces of objects that healthcare workers and patients touch, they help prevent the spread of infections.

It is really satisfying to get to interact with people as passionate about this problem as I. When I learn about their insightful approaches for combatting resistance, I become more hopeful about the ability of humans to continue living in the midst of bacteria. As players in this battle between humans and bacteria, it is frustrating to see our offenses and defenses stripped away as bacteria effortlessly evolve resistance, but as long as there are people motivated to keep fighting, I think we have a chance.

Fiction

2010-06-04T10:40:00.000-07:00

I've been reading a lot of fiction these days. I think that it is healthy to read fiction. It satisfies the human need for drama without actually causing any drama. (That is at least when it is read responsibly...there are times when I very much wish that I could read and drive at the same time. I haven't done it, except for once at a long stop light. It still felt dangerous even though the car was completely stopped. I swore it off. There is no need for the near fatal accident kind of drama in my life.) If more people read fiction, there would probably fewer gangs, murders, and wars. There might also be less drunk driving, theft, and vandalism. Go read some fiction everyone!

Among the books I have been reading is The Adoration of Jenna Fox. It covers zillions of topics I'm interested in, like the definition of life, brain injury, biotechnology and the laws that govern it, and surprisingly, antibiotic resistance. I sort of cringe every time I read a novel that attempts to cover science because I know more about science than most authors and I usually think that they got it all wrong. I am not generous. However in this book, I think that Mary Pearson got most of it right.

There are millions of people killed by an "aureus epidemic", which I presume is a reference to Staphylococcus aureus. In the book antibiotics made aureus evolve into a worse pathogen than it had ever been prior to antibiotics. It killed millions of people and brought on another great depression. As I was reading about teenage girls getting horrid infections, my first thought was "What were they doing?" since the populations most affected by S. aureus are methamphetamine using homosexual men, wrestlers and prisoners. Then I realized that the S. aureus alluded to in the book was a futuristic strain worse than anything currently around. So I started trying to figure out if that was possible. There are certainly more plasmids in bacteria now than in the pre-antibiotic era and those plasmids are picking up toxicity and virulence genes in addition to antibiotic resistance genes. The selection for resistance is probably what keeps the plasmids around and the virulence genes may expand the transmissibility. Indeed, bacteria are becoming meaner than they used to be (which has always been pretty mean). Honestly, S. aureus has probably already killed millions of people, not as an airborne epidemic (as it seems to be in the book) but as an epidemic that infects cuts, abrasions, and sites of surgeries. I decided it might be a long shot, but it certainly was possible and so I went along with it and enjoyed the book immensely.

The next book I started reading is the Kindle omnibus of Sherlock Holmes mysteries. I never enjoyed them much when I had the image of a stiff and boring logic machine playing the part of Holmes. I must admit though that after seeing the latest Holmes movie, I decide to give the stories another try with the character played by Robert Downey fixed in my head. It made a great deal of difference. Despite criticisms, I think that the updated version of Holmes is truer to the stories than the iconic dry and dull version. The original stories are wild.

I fully appreciated how wild they were as Doyle spun a tale in A Study in Scarlet about early Mormon pioneers. It is a story of harems, secret societies, secret murders, and absolute dictatorships. It is a great story, but I laughed though out the reading of it as I compared Doyle's version of the settling of Utah with the version that had been related to me by my grandparents. They were nothing alike. Doyle's was much more thrilling. At some point during the story, the idea came to me that there may be people who believe Doyle's account of Mormon pioneers as forceful, lecherous murderers, but I rapidly rejected that idea because it bears so little resemblance to the truth. That said, I remember some strange responses to things I have said which may suggest that there are people who believe that I grew up in some sort of harem. (I didn't.) I may need to test it out a bit and I might have some fun while doing so.

be beautiful

2010-06-03T13:37:00.000-07:00

I love this.

It is by Noelle Dass who sells T-shirts and other pieces of art online.

Perfect Day

2010-05-24T23:11:00.000-07:00

I am in San Diego with my mom having just finished a perfect day. We kicked around in the morning, ate lunch at a healthy vegetarian brunch sort of place and then went to the Mormon Battalion Visitor Center in the Old Town part of San Diego. We went because Maureen and Dan Thulin are missionary tour guides there. They are some of the greatest friends that the Barlow family has ever had. I have known them since I was 10. It was great to see them. Then, the highlight..... We went to the awards banquet where I was awarded the Siemens Medical Diagnostic Young Investigator Award. I was the youngest person there besides the two grad students who got awards. I didn't trip when I walked up to the front of the room to get my award. I ate sumptuous Sea Bass. I got paid a lot of attention by scientists who have been doing really good science for a long time. It was fun. I got bragged up a lot and my head got kissed a lot by a lot of people who are proud of me. And while I wouldn't want to do this every day (it wouldn't be special then), I find myself really hoping that I get to have a day like that again.

The power of pomegranate

2010-05-19T23:06:00.000-07:00

I judged an international science fair in San Jose last week. The projects were top-notch. Many of the high school students present had projects that would beat an average Ph.D. dissertation. Lots of the microbial projects were about antibacterial properties of herbs, seaweed, vegetables and fruit juices. There was one that particularly grabbed my eye. It was about acne. A student showed that pomegranate can kill Proprionobacteria, which are the bacteria that cause acne. She didn't come up with the idea on her own. Pomegranate is a traditional Korean therapy for acne, but little scientific research has been published on the matter. This student actually moved to Korea, attended a Korean High School and lived with family members in Korea so that she could work in a lab willing to let her study the therapeutic value of pomegranate. Her results were worth the effort. She did great work and even with no personal interest, I would have been very impressed. However, I also had personal interest in her study.

There is a reason that I have not posted any pictures of myself for about a year and that reason is acne. It's not bad enough for the dermatologist to give me accutane, but it is bad enough to give me antibiotics from the tetracycline family and a cream that burns my face every night when I use it and makes my skin peel like crazy. For all that, the cream isn't terribly effective and I hate the long-term use of tetracyclines for a couple of reasons. 1.) They don't break down in the environment and they accumulate in rivers and waterways, which ultimately dump out into the oceans near coral reefs. I hypothesize that they are part of the coral bleaching problem since antibiotics are known to bleach coral. 2.) I have a friend who was hospitalized for liver failure caused by long term use of tetracyclines prescribed for acne.

So, I have been looking for other treatments for acne. After seeing that science fair project, I went out and got some pomegranate juice and I have been drinking it for 4 days. Already, there is a big difference. I hope it lasts. If it does, I will blog more about it in a month or so and possibly with a picture of me showing off my beautiful and acne free face. :-)