Antimicrobial Resistance

Not on my watch

mbarlow@ucmerced.edu (mim) — Thu, 03 Dec 2009 22:27:00 +0000

I got a request to post information about the Kimberly-Clark Healthcare campaign against hospital acquired infections. The resources at the site are great! Very professional and scholarly. Check it out.

Global Dominance

mbarlow@ucmerced.edu (mim) — Sun, 11 Oct 2009 22:30:00 +0000

As I was thinning out my strawberry plants yesterday, it occurred to me once again that everyone really is trying to take over the earth and strawberry plants may well be on their way to success. The resistance genes I work on have already done it, though the ones I have created in the lab haven't (thankfully, copious amounts of bleach seem to prevent that).

In my own little way, I am also trying to take over the earth. I have had a little success because medical doctors now have respect for phylogenetics, and they didn't when I started. (I wasn't alone in that effort, so I can't take all of the credit.) Using phylogenetics to study disease is a pretty universally accepted practice and lot's of doctors cite my papers. Does that equal global dominance? Well, if it does, I am not sure why it is such a desirable thing...and yet, I am still persisting at it. Maybe it's just what we do as living organisms.

My next attempt at global dominance is to get some good microbial pop-gen theory developed and universally accepted. If the number of manuscripts I have planned actually get published, it could happen. Ha! Ha! Ha! Just remember you were warned and don't be too afraid in the meantime..... I'll be kind and generous (with my enormous UC furlough-reduced professor's income) if it ever does happen.

Synthetic Biology

mbarlow@ucmerced.edu (mim) — Sun, 04 Oct 2009 03:05:00 +0000

A recent article in The New Yorker entitled "A Life of its Own" included the following quotes about synthetic biology:

"For the first time God has competition." -Nature 2007

and

"What if we could liberate ourselves from the tyranny of evolution by being able to design our own offspring?" -Drew Endy

Synthetic biology is the science of engineering organisms to produce something or do something new. Genes from different organisms are brought together in a single organism to perform some new function.

The upshot of this article seems to be that the practitioners of synthetic biology can do a better job at creating/designing/selecting life than either God or evolution. That seems pretty arrogant to me...even for professors at MIT and Stanford.

As an evolutionary biologist who works at the fringes of synthetic biology by engineering and accelerating the evolution of antibiotic resistance genes, I am very impressed by the potential of synthetic biology. I attended a talk a couple of years ago amorphadiene, which is a precursor to artemisinin, an excellent antimalarial drug produced by plants. While this drug is affordable in developed nations, it is too expensive at 10 cents per dose for most Africans to afford. Jay Keasling was able to cobble together the genes and pathways necessary to get bacteria and yeast to produce amorphadiene. This has made the drug artemisinin affordable in Africa.

I think that this project is a small demonstration of the potential of this type of science. However, it is not the only demonstration of this type of science. Organisms have been cobbling together genes and pathways as long as they have existed. For example simple comparison of the genomes of most strains of E. coli with strain O157:H7 shows how different genes from viruses and pathogens have been assembled in O157:H7 to make it capable of invading and taking control of the cells of the human digestive tract. On a more positive note, the bacteria that are resistant to toxins and and able to help in bioremediation efforts often have numerous genes assembled from many organisms.

While I fully support the use of evolutionary tools by scientists to develop technologies that support human interests, I think it is dangerous when humans think that they are superior to natural forces. Billions of dollars have been spent to develop semisynthetic antibiotics with the thought that man could do a better job creating antibiotics than nature, but resistance to those antibiotics has developed more rapidly in some cases than resistance to naturally produced antibiotics.

A more worrisome aspect of drastically changing life without evolution is that deleterious effects of combining genes from different organisms can be ameliorated by mutation and selection as a new combination of genes spreads through a population. When substances are produced synthetically and then distributed throughout populations, their deleterious effects have not necessarily been detected or removed. It is possible that great harm could come upon large populations through synthetic biology because the purging process of evolution was eliminated.

More disturbing to me than the claim that synthetic biology is better than evolution, is the claim that it is better than God. When I watched Gattaca in high school, I thought that there was no way that humans would be able to pick the traits that they wanted their children to have. I thought that the movie was simple an overly imaginative writer going a little wild with sci-fi. However, the technologies that are necessary to custom build children exist now. They are not affordable or practical, but at some point they might be. It seems that artists and writers inspire scientists with wild futuristic ideas and that scientists make those ideas become reality. In a small way a scientist becomes a god in his or her laboratory....growing life and destroying it...proclaiming what is good and what isn't. However, as scientists do this, they are often dwelling within the confines of relatively small offices and labs where most of the problems that confront society don't exist. To most scientists the perception and purpose of God is limited to the first two chapters of Genesis where the creation of the earth is described. If the only purpose of God is to create, then I wonder why the rest of the Bible (not to mention other scriptural texts) exists.

I guess that there are a number of people whose knowledge of the scriptures is greater than scientists because they have expanded their scriptural repertoire to include a verse of John that reads: "Truly, truly, I say to you, unless one is born again, he cannot see the kingdom of God." (John 3:3). Those individuals go to war with scientists about whether God and evolution are real and I worry that ethical decisions about how the organisms with synthetically engineered functions or characteristics should be used and treated are given less and less consideration. Many people perceive cloned organisms as mindless zombies, when, in fact, a cloned human would be a real individual with and independent mind and emotions. If the time comes when human cloning is performed, I worry that those individuals might not be treated as well as non-cloned people. When scientists start declaring that their works are greater than God and evolution, I worry that the morals relevant in their own small universes might not be sufficient for society. I find myself hoping that they are not the ones who will be making the ethical decisions about what should be done with their work.

All Better!

mbarlow@ucmerced.edu (mim) — Mon, 28 Sep 2009 17:56:00 +0000

My dad is out of the hospital! He has returned to life as normal and he sounds good on the phone. I am going to visit my parents this weekend and I can't wait. It is nice to once again have the peaceful sense that all is well.

I am slightly tempted to digress into how Chlamydia pneumoniae (This is not the type that is sexually transmitted. It's airborne.) contributes to atherosclerosis, but I am in too good of spirits to digress into such dismal topics.

Xanthomonas campestris

mbarlow@ucmerced.edu (mim) — Fri, 25 Sep 2009 22:53:00 +0000

Mainly I have always know X. campestris as a plant pathogen that sometimes harbors resistance genes I'd like to study. It has taken on a new role in my life though, and is currently my favorite bacterium. (That is saying something.) X. campestris is the source of xanthan gum which is in everything from face scrub to ice cream. It is especially important for gluten free baking because it holds everything together and also holds the air bubbles made by the leavening.

After 2 month of going gluten free, I finally made it to a Whole Foods where I got some xanthan gum. (I ordered some 1 month ago from Amazon, and I probably would have starved before it got here. It didn't get shipped until today!) I have been eating a lot of foods that do not require baking or leavening, but after 2 months, I was practically dreaming of anything starchy besides tapioca, Chex cereal, potatoes and rice. (I like them but they just don't quite make up for no wheat.) I made a pancake this morning with xanthan gum. It was my second attempt at a pancake. The first one held together because of the egg in the batter, but it was dense and heavy and not good. I added a little xanthan gum to a combination of potato starch, tapioca flour, and corn starch, baking powder, yogurt, water, egg and salt. Yum! Heaven in a skillet. Honestly, it was even lighter than those I used to make with wheat flour, and the flavor was nearly the same. I ate strawberry freezer jam on it and it was simply delicious.

Ahhhh.... X. campestris where would I be without you? (Still having ridiculous dreams about Midwestern agriculture probably). I hope your brief life in food production fermenters is so happy. You certainly deserve it for your excellent contributions to food web.

Working Late

mbarlow@ucmerced.edu (mim) — Thu, 24 Sep 2009 05:17:00 +0000

I have heard a lot of evolutionary biologists say that religion is a crutch for those who are too emotionally weak to handle the realities of a harsh world. I am certain that is not the case for me because evolution is my crutch. My thesis advisor once told me he was amazed that when I was upset I could sit and unerringly set up dozens of experiments with tears streaming down my face. (I was always careful to keep the tears from falling into my experiments.) The reason I could do that is because lab work calms me down more quickly and certainly than anything else. Setting up experiments is a sort of meditation for me. It requires complete focus. It has a sort of rhythm to it, like breathing. It requires control of the body to stabilize hands, to left-handedly remove lids and pour liquids, and to maintain reasonably good posture for hours on end. The smells of the lab while not always pleasant, are at least familiar and comfortable and it is easy in that place to find the confidence and discipline necessary to work for hours at a time.

Currently, every cell of my body is aching to go to the hospital where my dad is recovering from a heart attack. But now isn't the right time. My dad is at the hospital and I couldn't see him much if I went anyway. They don't allow many visitors in his room. My mom is staying at the hospital with my dad as much as possible so I wouldn't get to see her much. He is recovering well and there are no farewells to be said at this point. It makes more sense for me to go in a week when my dad goes home and my mom goes back to work. They will need some help then.

Not to mention that I have work to do here...a journal article to review....a manuscript to submit...a collaborator who needs help preparing for an important talk.....bacteria to grow and then kill....students to advise and so on. But it is hard to really care about any of those things right now when all I want is to see for myself that my dad is okay.

Somehow in the midst of this, it is still easy to walk into the lab, and for the time I am in there, to fall completely into the comfortable routine of lab work.

MRSA on beaches. Ewwww.

mbarlow@ucmerced.edu (mim) — Mon, 14 Sep 2009 18:59:00 +0000

The ICAAC meeting is going on in San Francisco right now. I went to the beta-lactamse dinner last night which Robert Bonomo always organizes wonderfully. It is always good to go and meet up with friends who share a love of bacteria and specifically beta-lactamases. It is fun when enough nerds gather that we can even have sub-groupings of nerds. The best part is that we can discuss really disgusting infections while eating Italian food and no one even thinks that it is strange or revolting.

One of the grossest findings presented at ICAAC so far is that MRSA is found on beaches. I think MRSA is probably everywhere. What this means for every day living: Disinfect every scrape or scratch or abrasion you get. MRSA would just love to infect your wound, even if it is really minor. It is still okay to go places and play and even get hurt a little bit. It is simply necessary to be a bit more attentive to even minor injuries.

Polio Eradication Continues!

mbarlow@ucmerced.edu (mim) — Thu, 10 Sep 2009 18:50:00 +0000

Hooray! The Taliban has stopped preventing polio vaccinations in Pakistan. Global polio eradication is becoming very close to reality and when it does it will be the second disease eradicated from human populations. The major roadblocks preventing complete eradication are uncooperative governments.

Here is a link to a good article.

Qnr, A candy coated pill?

mbarlow@ucmerced.edu (mim) — Thu, 20 Aug 2009 20:00:00 +0000

Fluoroquinolones are rapidly becoming the most heavily consumed antibiotics in America. This trend started in 2001 after the anthrax attacks because ciprofloxacin was the only antibiotic approved for treating anthrax. Prior to time, beta-lactams (penicillin and other similar antibiotics) had been the most popular because of their low toxicity and activity against a broad spectrum of microbes. However, the patent life on most beta-lactams was running out so marketing of them was decreasing. The timing of the anthrax attacks and the waning hype for beta-lactams created the perfect opportunity for fluoroquinolones to move to the forefront of prescription formularies.

Fluoroquinolones kill bacteria by inhibiting the exzyme known as DNA topoisomerase. That enzyme releases supercoiling tension as the double helix is unwound during DNA replication. If that enzyme is knocked out, the DNA gets tangled up and breaks and the cells die. Bacteria have a few ways of protecting themselves from fluoroquinolones. Their cell walls can mutate so that they become less permeable to the antibiotic. They can express efflux pumps that export the antibiotic from inside them. They can also express the gene qnr. The Qnr protein, encoded by that gene binds to DNA topoisomerase and prevents fluoroquinolones from doing so. However, the topoisomerase can still perform its regular role of relaxing supercoiling tension so the cells don't die.

I have been doing some work on qnr and it turns out that there are some tricks in manipulating the DNA encoding a gene that is involved in the manipulation of DNA. I sometimes wish that genes were large enough that I could throw them on the floor and stomp on them when they start playing tricks on me the way that this one does. I sometimes also wish that I could purify enough DNA so that I could taste it. In High school, my biology teacher told us that DNA is candy-coated (referring to the deoxyribose sugars that make up its backbone). I often wonder if it is really sweet. Some days, I very much doubt it. It might be easier to have an agreeable relationship with qnr if I knew there was some positive aspect to it.

The picture below is a portrait of me working on qnr. (I'm not the hand)

A deadly illness in African children

mbarlow@ucmerced.edu (mim) — Mon, 10 Aug 2009 16:19:00 +0000

There is a great article in Time about zinc and its effects on children suffering from diarrhea, which is one of the deadliest illnesses among African children.

Airplane Etiquette

mbarlow@ucmerced.edu (mim) — Sun, 09 Aug 2009 04:59:00 +0000

For the first time in my life, I think I failed in citizenship. When I was a kid, it was assumed that my school report cards would ALWAYS have satisfactory or outstanding marks in behavior. They always did. I am not sure if this was because I was a good kid, or simply because I was a quiet kid, but I tended to stay out of trouble with the teachers. However, at the age of 32, I think I finally experienced what it would have been like to get a "needs improvement" or "unacceptable" in behavior on the plane I was on yesterday.

It all started while the plane was sitting on the tarmac with the door closed and the ventilation on, but for some reason we weren't going anywhere. I was working on my laptop on some diagrams I am drawing for a manuscript. There had been no announcement at this point to turn off electronic devices, but when the flight attendant, (a middle aged woman with salt and pepper hair named Lilly) came down the aisle and asked me to start shutting down my computer, I promptly saved what I was doing and put my computer to sleep. I slid it into the nifty vinyl cover I made for it and stuck it in the seat back pocket. After several minutes, we were still sitting there and I got bored. I decided that since electronics were not allowed, I'd paint my nails blue. After all, I was flying into Seattle and spending the day with my sis-in-law there and blue nails seemed like a fine way of celebrating. I pulled my computer back out and used it and it's great vinyl cover as a surface for this small project.

I had just completed the left hand when Lilly walked by again and asked me to stow my computer, which I did. I needed to finish painting my right hand so I pulled out a magazine and used it as the new surface for my manicure. I had just finished the right thumb and Lilly was back telling me that actually I shouldn't paint my nails on the plane at all. I closed up the nail polish but we still weren't moving and I got bored again so I started thinking.

It's always a dangerous thing to think. I started wondering why I couldn't paint my nails on the plane. The ventilation was on, so I seriously doubted that the fumes from the polish were bothering anyone. I couldn't smell it and I was the one closest to it. Besides which, people wear perfume, pass gas, drink alcohol and coffee, and vomit on planes and all of those smells are worse than nail polish (in my opinion). Perhaps a matter of safety then. After all, nail polish can be flammable when held over extreme heat. My thoughts went back to the point about people drinking alcohol and passing gas on airplanes and that both alcohol and methane are more flammable than nail polish. So it clearly wasn't a safety issue. Perhaps the flight attendant was worried that the nail polish would spill, but then I thought of all the drinks that get passed out and decided that fear of spilling things is not a concern on planes. The only logical explanation left in my mind, was that Lilly hated me polishing my nails because the polish was blue. I decided that the color was none of her business and since I felt as conspicuous as Michael Jackson in one sparkly glove with only six digits painted blue, I decided to paint the other four. We had made it to the safety demo part of the flight so I figured the flight attendants wouldn't stop in the middle of that over a small matter of nail polish and so I opened the bottle up. Before I could even get the brush out, the woman sitting next to me starts saying in a very shrill voice "You idiot! she just told you not to polish your nails on the plane! Didn't you hear her? Put that up now or I will call her over! Do you want me to call her over here?!" I put the polish away. The woman seemed to think it was a life and death matter. Clearly not worth it.

When the safety demo was finished, Lilly was back. Not over the nail polish since it was out of site this time because y bag wasn't tucked under the seat in front of me far enough. It was under there as far as anybody else's, but I pushed it under a bit more. I wasn't feeling particularly helpful at that point so I didn't go to heroic efforts to push it under very far. The flight attendant was insistent that it go under farther and when I refused on the ground that the plums in the side pouch would get smashed she said she'd stick it in the overhead bin. I pulled the bag out, and started to close it up as she was trying to yank it from my hands. When I finally surrendered it to her after closing it up, she verified the presence of the plums in the side pouch and put it up. Shortly after the fasten seatbelt sign went off, I retrieved my bag and observed that Lilly had place my bag precisely at an odd angle where the slamming door of the bin would smash the plums.

Throughout the flight, I was trying to remind myself that refusing to let the woman next to me get out to use the restroom would be unnecessary and that tripping Lilly could get me charged with assault. The woman next to me tried to demonstrate that she was nice by emphasizing her please and thank you when she asked me to let her out of her seat. I remained silent and let her go, though I felt like telling her that once she has called a person an idiot she should give up a façade of niceness as it has become entirely useless. At some point in the flight, she started passing a lot of gas and I turned up the airflow and noticed her sinking lower and lower in her seat throughout the remainder of the flight. Perhaps her thoughts were also visiting the relative volatility and flammability of various chemicals.

At the end of the flight, Lilly was once again hovering over me and she glared for a full thirty seconds at my bag which was once again stowed under the seat in front of me. I refused to acknowledge her and she finally left without speaking.

Miriam vs. Science!

mbarlow@ucmerced.edu (mim) — Tue, 04 Aug 2009 17:06:00 +0000

Science is frustrating and consuming so it tends to attract creative people with high pain tolerance and screwed up priorities. Scientists are the sort of people who need difficult problems to keep them occupied. I have heard many scientists postulate that the government funds science just enough to keep us all busy and off the street, but they don't pay us well enough that we could really do any real damage. I guess the inference is that there is a conspiracy to actually keep scientists frustrated and deeply occupied to protect society from bright, but screwed up people.

When science gets really frustrating, all scientists come up with strategies for coping. Some people shout at their equipment. Others shout at their students. But many scientist get more creative than that. My friend, Steve Salipante, made all of us come up with kill faces and assume Berserker identities. He also had a tally sheet on the wall of us vs. science. Each of us got a point when an experiment worked and several points if there were lots of steps leading up to the success. Science got a point every time anything failed. Science was always ahead....Always.

Recently, At PARC I saw a scientist wearing a "Game Over" t-shirt, which turned out to be pretty appropriate because not even the controls for our experiments were working that day. I am tempted to order one for everyone in the lab, except it might be bad for morale.

I tend to be a bit stoic about frustration in the lab. I try to cheer everyone on and encourage them. Then later on I go and demolish something in the name of home improvement. Usually it works out okay in the end. (Both the science and the demolition.) Good thing I have a 65 year old house that needs some improving.

down time

mbarlow@ucmerced.edu (mim) — Sun, 26 Jul 2009 02:10:00 +0000

I wasn't sure whether I'd be working in San Diego at Scripps, in Palo Alto at PARC, or in Merced next week. All have their advantages. At Scripps is an instrument I need to use, in Palo Alto is another instrument I need to use, and in Merced is my own bed which I have been missing.

It's always horrible when experiments give a scientist ambiguous results, but sometimes the results of the ambiguity are really nice. I have ambiguous results which means that experiments are put on pause to design some more and different experiments to shed some light on the confusion. The result of that is that I get to spend at least a few days here in Merced. I have 1 technician who needs some help with her own strange results, 2 manuscripts to revise, and 3 undergrads who need some attention. I am also very tired as I have gone for days without much sleep. It is good to be back in Merced for a while.

So I am sitting here hoping I don't die

mbarlow@ucmerced.edu (mim) — Thu, 23 Jul 2009 19:06:00 +0000

A bunch of grad students invited me to go pick blueberries with them during a break between sessions. They offered me a berry to show me how good they are. After I ate it they said "Oh ya and Tony ate one about 10 minutes ago and he's still alive so you'll probably be okay." Then they reassured me that they were absolutely certain that those were blueberries, they just hadn't tried them yet. At that point, it seemed like the best plan was to go berry picking and have some fun whether I was on the way out or not. I am still not dead so it will probably work out okay. If none of us are dead by tomorrow, the plan is to eat them over cereal for breakfast. Yum. I am posting pictures of the people who are either now assassins or new friends.

Xiao Ye (he's the one who gave me the berries) and Martine Ehringer

And William Ratcliff

Science Summer Camp

mbarlow@ucmerced.edu (mim) — Tue, 21 Jul 2009 12:38:00 +0000

These are some photos of the beautiful New Hampshire backwoods where I am staying.

Two years ago, I found a wild Orchid. This isn't quite as good, but I still like it a lot.

Gordon Conference

mbarlow@ucmerced.edu (mim) — Tue, 21 Jul 2009 03:10:00 +0000

Well, I am in the backwoods of New Hampshire at what my mom calls "Science summer camp" which is a pretty accurate description. The shared showers, thin twin beds, and wood paneled walls with green trim add to the ambiance. I may be advancing through the ranks of the Gordon Conference. I got a private room this year. It is still in the same dorm as the graduate students, but at least I don't have to share a room with anyone this time. The housing is arranged by age, but maybe rank is considered as well.

Many of my friends are here. Merijn Salverda, Pilar Francino, Dan Weinreich and Tony Dean are all here and it's good to see them. I have also run into many people I have become acquainted with, but don't see that regularly. After getting out of one of the sessions, one such acquaintance said to me "Most of those talks were spun off of experimental evolution work you've done, weren't they?" Even small acknowledgements are encouraging.

I am often told that I am an iconoclast because I publish science as it is. I don't worry a lot about the paradigms that others adhere to if they don't apply to my work. This approach makes science more fun and exciting, but also puts me so far outside the mainstream sometimes, that it takes about 10 years for others to accept those iconoclastic ideas, and by that time, they have forgotten who came up with them. Sometimes I want a poster of myself entitled "The Iconoclaster". I would have muscles bulging through a labcoat and pipettemen in holsters at my hips. Maybe it would scare people into remembering who came up with what. (Okay fine, it probably wouldn't, but it would be fun anyway.)

Tomorrow we are having a semi-spontaneous sub-conference on beta-lactamases. This should be fun. I was one of the people who made beta-lactamases a model system for studying evolutionary biology. Two years ago, the sub-conference included me, Merijn and Dan. This year, it seems that there might be as many as 10 who want to attend. Who knows? Maybe two years from now, we'll get a whole session of the real conference. (Dream big you know.)

All summer in a day

mbarlow@ucmerced.edu (mim) — Tue, 14 Jul 2009 17:33:00 +0000

It has been a while since I have had a day off. I am working at the Palo Alto Research Center for a while (possibly until mid-August) and we (Michael Recht and I) are scrambling to gather lots of data in a little time. Consequently, we have been working long days in a cold, loud, windy room doing lots of trouble shooting. We have been fairly successful. Our troubles are not lying dead in the street, but they seem somewhat subdued for now.

We have some real data in which we are confident. Real data are like the drugs that keep scientists hooked to relentless schedules like the one we are working on now. We sleep, eat, and collect data. I am dead tired, but running off the buzz of really cool data. However, I have a glorious half hour to sit and do whatever I want because we took some time out this morning to think, which put us off schedule. If we were to start our experiments right now, we would miss lunch in the cafeteria. I brought my lunch, but Michael didn't and it's Mexican food day which is pretty good. Though it would be nice to skip the eating part of our lives right now, that really isn't practical. I am glad to have a half hour to simple sit.

I realized that I will not be doing anything this next Saturday besides getting ready for the Gordon Research Conference on Microbial Population Genetics which is in New Hampshire next week. My time prior to this Saturday is completely scheduled, and from the moment my plane touches down in San Francisco upon returning from the conference, my time is scheduled. (Yes, I will be in the lab at the end of a traveling day which includes taking a shuttle to Boston, a flight from Boston to SFO, and a 2.5 hr car drive back to Merced).

I am not sure what I will do this Saturday. My sewer line should be completely replaced by the end of today and I am not sure what my backyard will look like when I return, so maybe I'll put it back together. I am sure I'll do a couple loads of laundry. Maybe I will take a nap or read or go for a walk or watch Hmong guys play volleyball with their feet. All of those sound great right now.

I did forego some sleep last night and went dancing in Palo Alto. The music was Latin and I taught a couple of guys to Merengue. It was fun. I noticed that all of the women in this area have long hair that is really shiny with at least a few curls in it. I showed up with my short (though stylish) hair, blue fingernail polish and a cute shirt depicting a small child about to be eaten by a sea serpent. I felt like the entire counter culture population present and had a good time regardless.

You have got to read this article!

mbarlow@ucmerced.edu (mim) — Sat, 11 Jul 2009 17:38:00 +0000

This article "Unsung heroes work hard to cut hospital acquired infections" documents great advances in the fight against antibiotic resistance! My brother Tom, a doctor, just sent it to me. Very important stuff as antibiotic resistant nosocomial infections kill more people in the US each year than HIV does.

Hot Stuff!!!!

mbarlow@ucmerced.edu (mim) — Sat, 04 Jul 2009 22:58:00 +0000

I just got a cool post on my Facebook Wall from Marnee Chua, the development genius who raises funds for the School of Natural Sciences at UC Merced. She informed me that her homework assignment from her online course through Montana State was to read the article "What Antimicrobial Resistance Has Taught Us About Horizontal Gene Transfer" by Miriam Barlow. It is a chapter in the book Horizontal Gene Transfer:Genomes in Flux. That is the first time a friend has told me that someone I have never heard of referred them to my work. It feels so good to know that someone out there reads and appreciates my work.

New Directions

mbarlow@ucmerced.edu (mim) — Sat, 04 Jul 2009 02:14:00 +0000

I have been working on antibiotic resistance for nearly ten years now, and I definitely still love it. It is a great system for studying evolutionary biology and it feeds my morbid sense of humor. However, I find that after a decade, my attention wanders a little and I am venturing out into some new directions.

I am starting to study math a little with a brilliant woman, Kristina Crona. She thinks that antibiotic resistance can teach her something about math. So I explain biology to her to help her with her math problems and then I get her to explain math to me and it turns out that some of my problems are interesting to her. She is so good at explaining math that it seems easy and fun while she is around and it still makes sense after she has left. That's a good mathematician.

I have also started working on a coral reef project with Monica Medina. We are trying to push the evolution the symbionts of coral species to find out whether they can adapt to changing ocean conditions. This is fun science. I am more excited about this project than anything that I have done in the lab for the past year.

I am also starting to work on biofuels. This line of research may be the most challenging because it requires a knowledge of chemistry. I have taken more chemistry classes than biology classes because chemistry is so challenging to me and I am always trying to overcome that deficit. It is good to have a challenge and I think I can work this project out. It may just take a lot of planning before it becomes anything approaching brilliant.

The journey of motherhood

mbarlow@ucmerced.edu (mim) — Tue, 23 Jun 2009 16:50:00 +0000

My sister Marie is due to deliver a new baby very soon, which means that my caring and protective feelings for her are amplified by a factor of at least ten. I am perfectly content to massage feet, trim toenails, carry luggage, set up the nursery, and watch Youtube videos of Criss Angel as a show of support to my sister. These protective feelings extend beyond her however. Last weekend, my show of support for a friend's expectant wife came in the forms of baklava, galatabouriko, dolmas, spanakopita, olives, cheese, salad, and bread because she wanted Greek appetizers at her baby shower and I am experienced in Greek cooking. Beyond that, I have recently been recruited as the on-call doula for two mothers whose husbands may be out of town when they go into labor. I have not been a doula since I was 19 and helped with the delivery of my cousin/best friend's baby, but those moms seem to sense my protective nature and say that they would trust me perfectly to care for them while they are in labor.

As I try to reason through my compulsion to care for pregnant women, I find reason is perhaps lacking. All I have is an idea that pregnant women go on a painful and dangerous journey that lasts 40 weeks. The destination seems to be the border between spirits and the living where there exists a passageway for life to come into or exit the world. A woman, it seems, must brush against death as the final step in collecting a new life at that point of passage.

While the journey in takes 40 weeks, the journey back takes much longer as nearly every facet of health and life is delivered from mother to child. Food, warmth, support, love and learning are all provided by mothers who care for their new child with such strong compulsions that reasonable needs like sleep, privacy and personal interests are set aside.

This part of the journey is where my sister Marie has found her passion. During the first two days of her first child's life, she tried unsuccessfully to breast-feed her daughter after a C-section delivery. Through the help of a lactation consultant she was able to figure out the problems preventing successful feeding and to then find ways of solving them. In short, she fought very hard to be able to breast-feed her daughter and was ultimately successful. Her success ignited her with a desire to help others do the same. She has become a lactation specialist for WIC and energetically calls mothers encouraging them to do the same. There is no judgement or criticism if they don't do as she has done. She just tries to share with others something she believes in and that she has fought hard to obtain.

It is great fun to sit around the dinner table and hear her oldest daughter (now 5) discuss the technicalities of breast-feeding with unerring accuracy. It's even more fun to see the forms my sister's passion takes as she prepares informational packets for new moms and cupcakes decorated like breasts for doctors to increase their awareness of breastfeeding. She always emphasizes to me that WIC promotes breast-feeding because it supplies babies with natural antibiotics and that breastfed babies are healthier than those fed with formula. She finds a way of relating breast-feeding to everyone. As I watch the intensity of her efforts and the joy that she finds in them, I am in awe of her. Though I feel so protective of her, she is clearly one of the strongest and most fearless people I know.

This I believe

mbarlow@ucmerced.edu (mim) — Fri, 19 Jun 2009 16:52:00 +0000

About a year ago after having three grant applications declined in a week and a half, I started thinking about what things I believed in. I was inspired to do so by the NPR "This I believe" program and it seemed like it should be simple enough to define my beliefs, but it turned out to be enormously challenging. This essay was the best I could come up with, and for many reasons, I wasn't ready to share it. I pulled it out last night, cleaned up the writing a little and I think that it is something I can share now.

This I Believe
I believe in accomplishing the most important thing each day. I learned this while I was in graduate school from Kay Whitmore who was an ex-CEO of Kodak. I knew him socially outside of school and at some point, maybe a year after meeting him, I realized what an amazing opportunity it would be to have this man mentoring me. So I went to him with all of the questions I didn’t have answers for and he had answers for each one of them. When I was frustrated with school and ready to quit it was “Toughen up”. When I needed to go to a conference about evolution and didn’t have any money, he helped me find a sofa that I could sleep on in a comfortable home near the conference. And when my heart was broken, the answer he gave me was two tickets for the best seats at the symphony so that I could move on. The best answer he ever gave me though was when I asked him how to do well in life. He told me to accomplish the most important thing each day. He said that this was how he had become successful.

I took those words to heart and they did wonders for me. I got a Ph.D. in three years and published seven papers in that time. I raced through my postdoctoral studies in a year and a half and got a job as a founding faculty member at the newest campus in the University of California system about three years ago. With that position, I have helped to set up a genomics core as well as my own lab, published several more manuscripts and devised a way, at least on paper, of controlling antibiotic resistance and keeping antibiotics useful for an infinite amount of time.

Those words “accomplish the most important thing every day” would seem flawless to me if it weren’t for the fact that I seem utterly incapable of getting a grant. To a scientist, grants are life-lines. In essence, they are arteries carrying oxygen, water, and nutrients (literally) into the lab. Like blood to the body, money keeps research in a lab moving...progressing. I’ve been trying to get a grant for three years and most of my applications don’t even get scored which means they are in the bottom half. I have worked on becoming a better writer, generated data that make my proposals seem likely, and I have had scientists with grants read my proposals and edit them until they like what I have written. I don’t know what else to do.

The main source pumping money into research is the federal government, and since the war in Iraq started, there hasn’t been as much money for science as there used to be. But this may not be the only reason I can’t get a grant…I know people who get grants...Maybe I am too young, maybe I haven’t published enough, maybe I don’t know the right people, maybe antibiotic resistance isn’t as popular as H.I.V. or A.D.D. though it kills more people, and maybe it’s that I am trying to solve the problem by manipulating evolution instead of just making more and more drugs that are less and less effective.

With all of these unknowns, I want to call Kay Whitmore, or better yet, go visit him and tell him that I can’t get a grant and ask him what I should do, but I can’t because he is dead. He died of leukemia nearly five years ago. I found out about it from a newspaper article on the day of his funeral. I was in the lab and the most important task of the day ended up seeming meaningless as I sat there and cried.

I remember an address he gave a few days after the September 11th attacks in which he said ” There is no sense in death. Some people will try to say that God needs the dead more than we do, but try telling that to a widow with three children.”

I don’t know that my need really compares with that widow either, but as the money in my lab slowly runs dry, I feel like I need to talk to Kay Whitmore pretty badly and since I can’t, I just hang on and keep believing in the best answer he ever gave me.

I still believe in that advice my friend gave me. I am not yet funded, but seem to be getting a lot closer. My real reason for posting this though is that I went to a business school named for Kay Whitmore and looked at the display about his life and career that was set up inside of a glass case. It was all impressive, but there was nothing there about how involved he had been in helping college students. I was not the only one he cared for. He spent most of his time post-retirement working with students and he attended many recitals and graduations. He gave out much dating advice that always started with the line "Men are like microwaves and women are like crockpots". He was a guide and friend to so many. I felt like I needed to pay tribute to him even if it was only in this very small way.

new antimicrobials!

mbarlow@ucmerced.edu (mim) — Tue, 09 Jun 2009 18:29:00 +0000

This isn't much of a blog entry especially after taking off from blogging for a month but this is worth blogging about. A DNA binding molecule can kill bacteria in 2 minutes. This seems like a good idea except that I wonder what it does to human cell. I mean the same is true of heat, bleach, and peroxide, but those are all lethal to human cells too. Anyway, this is a cool idea.

Swine Flu, Red Mars, and Merced

mbarlow@ucmerced.edu (mim) — Thu, 30 Apr 2009 16:55:00 +0000

I went away to Utah and Mexico for a couple of weeks. I was really sick when I left and for the Utah part of the trip. I had a fever and my tonsils were swollen and I lost my voice. I shared my infection with at least one friend and both of my parents (I'm really sorry). Upon returning from Mexico, my friend accused me of starting the swine flu pandemic. I also was called upon to be the campus expert on swine flu in case the local press wanted to ask someone at UC Merced about it. As the campus expert and potential source (according to some) of the infection, I though I should post something about it.

Swine Flu is (usually) a Type A influenza that causes fever, runny nose, sore throat, lethargy, lack of appetite, coughing, diarrhea, nausea and vomiting. It is treatable with oseltamivir and zanamivir, which are neuraminidases that prevent the emergence of virions from human cells that have been turned into viral manufacturing plants. Unless an individual is immunocompromised, s/he should probably not take the antiviral medications because viruses evolve resistance to antimicrobials fairly quickly.

The current flu pandemic is not technically Swine flu but a chimera of human influenza, avian influenza and two strains of swine influenza. Apparently its symptoms are mild and it is not nearly as deadly as the press has reported. Currently, only 9 fatalities resulting from the current flu pandemic have been confirmed by the world health organization. This is fortunate, because the number of fatalities reported by the press would mean that the current pandemic is more deadly than the 1918 flu pandemic. However, it is not anywhere near as deadly, it is just easy to blame the popular.

I have started a new book I think I will like...Red Mars by Kim Stanley Robinson. Okay so the reason I started reading this book is because yesterday I got invited to a reception that the Chancellor is holding for him tonight and I wanted to at least get an idea of what he has written. I am only a few pages in (I started reading around midnight and my eyes were too blurry to last very long) but it already seems good. He has mentioned the search for microbes on Mars within the first few pages and that seems good to me. I am curious about how closely the exploration and terraforming of Mars will resemble current efforts by NASA.

And finally, the best news in a long time. The Army Corps of Engineers approved development of the Virginia Smith Trust lands for UC Merced today. It has been a long, hard battle to get the approval. Now we can build the university and sell some land to developers to provide scholarships for the students. Most are first generation college attendees from ethnic minorities and among them are some of the brightest students I have ever known.

Avoid the syph!

mbarlow@ucmerced.edu (mim) — Mon, 30 Mar 2009 17:18:00 +0000

My little sister sent this. I laughed for quite a while.