Love your bacteria

I thought this was an interesting piece on the role of good bacteria on our skin and how washing kills a type of bacteria that is very good for skin.

http://www.nytimes.com/2014/05/25/magazine/my-no-soap-no-shampoo-bacteria-rich-hygiene-experiment.html?_r=0

Bacteria used to be a bad word, but I think people are beginning to realize that 99% of bacteria are good and if you get rid of the good ones, the bad ones can proliferate. Of course, there’s the data that kids growing up on a farm or with a pet have a lower rate of allergies. Dirt is good; however, when it comes to personal hygiene it’s interesting to dig into all the cultural dogmas wrapped into it. I only bath my kid about once a week/ when he smells and never felt compelled to do it more frequently than that as it usually takes kids a while to start smelling. I’ve never done the hand sanitizer or antibacterial soap thing- mainly because I know that soap alone kills bacteria so it’s marketing gimmick. Now I’m thinking, maybe I should lay off the soap. The other reason is my theory that our immune systems were created for a reason- to kill stuff, and if you don’t have enough for your immune system to do it gets bored and starts in on bad patters like autoimmune disease and allergies etc.

I’m hoping the next word that have a cultural shift is “chemicals”. “Chemicals” seems to have been equated with all things bad and “unnatural” these days. I think the world (and internet) would be a different place if more people took several semesters of college and graduate level chemistry courses, but alas, a whole industry would be put out of business. We are made of chemicals and chock full of hormones. Even little baby boys are pumping out their own steroids that actually make their brain develop into the masculine type brain. Give me an organic beet and I could isolate the chemical that gives it the red color and the structure looks very similar to a red color made in a lab. Your body is its own little lab churning out chemicals and hormones 24 hrs a day. Acid is acid whether it comes from vinegar or from a different bottle -it’s chemical that likes to donate protons. Of course there are certainly bad chemicals-  ones that trick your own hormone receptors into activating or toxins. DES, agent orange, pesticides, stuff that leaches out of plastic… all bad ideas. I’m personally very impressed with my liver as I was injected with known toxins- chemotherapeutic agents on several occasions, yes, it was awful, but my liver took care of it and my body healed itself. One of my chemotherapy agents could have even been derived “organically” as it comes from the bark of a type of tree in Oregon. Fortunately, they synthesize it in the lab these days so “no trees were harmed” for my cancer treatment. If detoxifying required conscience actions on our part we would all be dead already. Take a moment and thank your liver and your kidneys for detoxifying all day long, 24 hrs a day without even having to follow a recipe on Pinterest!

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My Regular 6 month oncologist visit

I went to my regular 6 month check up Wednesday and it was the most boring check up yet! No blood work. My next visit in 6 months is with his nurse practitioner and not him, which is significant downgrade on vigilance for recurrence. I will only have annual exams with him now! It’s been about 2.5 years since I ended active treatment. Another thing that’s good is that I think all the bad stuff I attributed to Tamoxifen, which I will likely be on until I die of old age, seems to have been related to the long road of recovery from chemo. I hardly notice it anymore! You never “get back to normal life” after treatment- it’s finding the new normal, but I’m extremely grateful for not having to face more treatment!

MollyN’Will- I love weddings!

My cousin Molly married Will this past Monday. It was a sweet and fun time located at the beautiful Elm Bank estate. I was reflecting on that not only am I blessed with a great immediate family, but I have an excellent extended family too. Watching Molly come down the aisle with her mother and father, memories of when she was 2 and I was a little kid (8 maybe??) and hiking with the three of them. Time has passed, but in a sense, it hasn’t. That is what is special about family friends may come and go through various life phases, but family is family and provides continuity and it’s fun to look alike generation after generation. So, last night we danced the night away (especially Nehemiah who put on a few dance solos), with the people who have known me my whole life: my immediate family mom and dad, Tim and Leah (though it seems like I can’t remember “pre-Leah”), my very special Aunt Deborah, Molly, my array of uncles: Lenny, Ron, Marty, Kevin, and Gordon, my Dad’s cousin Bev & Don. Of course, family members can choose to not be a part of each other’s lives, but I guess through all our stages, we are the ones who have chosen to stick together, keep tabs, take care of each other during illness and tragedy, and celebrate the joyful times together.

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Writing Zombie

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Writing as a profession sounds so romantic. Visions of a cabin in the woods or on the ocean in the Florida Keys with a fisherman sweater, beard, and pipe come to mind… but alas…. that is not so for me. I write science. Last weekend, exhausted on a beautiful Saturday afternoon in May, I was in my son’s twin bed writing and eating out of a jar of peanut butter. I write at work. I write on the train. I write in bed at 4:30 am. I write in bed when my son goes to bed. I write on my couch… and apparently, I write in a toddler bed. When I drive my car, I think about what I am going to write. For the past 5 months, I’ve been working on four grants. The last for this round is due in 3 weeks, then I will take some vacation, and return so I can write… manuscripts.. I have 3 now piled up that need to be published.

Very few people actually know what I do. What I do can change from year to year and month to month. In 2012-13 we had a huge grant where I spent 6 hrs of the day on my feet or running down a hall. It was physically grueling, but great for recovering from breast cancer treatment because I didn’t need to think a whole lot. It was kind of like shift work with some thinking to problem solve the mitochondrial respiratory assay that wasn’t working… Now with all the sitting I do, I look for opportunities to walk or stand. I’m not sure how much longer my back can take it. I’m trying not to covet the walking desk a PI has down the hall from me.

When I tell people I’m writing grants some think it’s like writing a grant to get a piece of playground equipment… or some undergraduates say they write grants in college (sure….). I always wonder what that means when an undergraduate or recent graduate claims they did grant writing for a lab they were in….. did they write some of the administrative pages…. find some papers for the person who actually was writing the grant (the PI)… get the PI coffee???

So here are some scientific writing factoids:

1. You have to have data to write anything. Unlike writing fiction, no one wants to hear from you unless you did an experiment and have data.

2. This means you have to, a.) design good experiments (requires synthesis and knowledge of vast bodies of literature), and b.) get things to work in the lab (problem solve), have skills, and work and/or get other people to work (management skills), and c.) CREATE! Yes, being a scientist is creative, but very few people understand what you created. Rare is the patient who knows the scientist that created the treatment that cured their cancer etc. It’s like top secret art that very few people will ever appreciate… the opposite of performance art.

3. Everything has very specific space limitations. Therefore, even though I would like to wax eloquently on the subdural space and if there is actually a space and summarize an interesting literature review I did on the anatomy 5 years ago- it won’t fit. Being a scientific writer means that you read every other type of literature and edit in your mind all the words and details you would remove. I am about to finish Oliver Sacks’ “The Mind’s Eye” and I can tell you that he has not written scientifically. Yes, he is a very interesting neurologist who writes large volumes about science, but has not published scientific papers. If he had written scientifically, his books would be 75% shorter.

4. The current average age for a PhD at the time they get their first RO1 is age 45. An RO1 is the standard large grant from the NIH for a single scientist somewhere in the ballpark of $5 million over 5 years. Once you have an RO1, you are considered an independent scientist. Therefore, let’s say you get your PhD at age 27- it’s another 15-20 years of training! It used to be one postdoctoral fellowship (3-4 years). Then it was standard to have 2 postdocs… and in this current funding environment a PI may have a handful of scientists in their lab working towards their first RO1. As a result, there are an ever increasing amount of “training grants” to get you from the postdoc to your first RO1. This is what I’m working on now. To get an RO1, you need dozens of publications and have generated good, interesting data that will impact human health.

5. The grant body of my current grant has 12 pages limit.

6. I have spent about 250 hrs on those 12 pages- so far. it’s dense.

7. The entire grant application will be about 100 pages total including 12 letters of support and administrative pages. Learning how to do all the administrative pages and budget work etc. is quite the undertaking if you’re in a small lab who does not have a person who specializes in that. Fortunately, I have had lots of experience doing the administrative pages for other’s people’s grants and a few for my own applications.

8. The NIH instructions for the grant given by the NIH including all the instructions for the administrative pages is 200 pages long. If you are proposing experiments that involve people (clinical trials), there is a 100 page supplement of instructions. I have a writer’s workshop manual on how to specifically organize each section that is 170 pages long. About 30 pages of this manual is instructions on how to write the specific aims page that is 1 page. It has instructions for every sentence on that 1 page.

9. The average reviewer will spend 15 minutes reading your grant.

10. I don’t have stats for the success rates of grants, but you have to be the persistent type and not be afraid by the possibility of failure nor discouraged by failure.

11. As my boss says, “the difference between those that accomplish things and those that don’t is those that accomplish things do it.” My PhD advisor liked to “brute force” approach to science- experiments… publishing papers… grants.  After this round of grant writing, I may come up empty handed, but in the process have honed my skills of grant writing.

12. You learn by doing.

What is compassionate when a brother is sinning?

“Reproof is unavoidable. God’s Word demands it when a brother falls into open sin. The practice of discipline in the congregation begins in the smallest circles. Where defection from God’s Word in doctrine or life imperils the family fellowship and with it the whole congregation, the word of admonition and rebuke must be ventured. Nothing can be more cruel than the tenderness that consigns another to his sin. Nothing can be more compassionate than the severe rebuke that calls a brother back from the path of sin. It is a ministry of mercy, an ultimate offer of genuine fellowship, when we allow nothing but God’s Word to stand between us, judging and succoring. Then it is not we who are judging; God alone judges, and God’s judgment is helpful and healing.  Just because God’s Word judges, it serves the person. He who accepts the ministry of God’s judgment is helped.”

― Dietrich Bonhoeffer, Life Together: The Classic Exploration of Faith in Community

My slugger

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Every kid has a knack for something. My nephew, Micah, is a detail and fact person. Not only does he remember what he bought his cousin for Christmas 3 months ago, he remembers to keep it a secret. Nehemiah can’t keep secrets, but it’s OK because he doesn’t remember enough facts to divulge secrets. My niece, Hannah, is teaching herself to read at age 4 and I am sure she will surpass Nehemiah’s reading ability within the next 6 months. He is 7. My kid’s particular knack is gross motor control and coordination. He learned to walk at age 1 as normal, started running a week later, and was climbing stuff at 18 months. When at a playground parents seem to hover anxiously glancing at me in concern that he is about to fall off a piece of playground equipment, but I know that he. just. does. not. fall. He had a balance bike at age 2 and taught himself to ride a bike at age 3 without training wheels refusing to let me help.

Of course we play around and he is always busy doing something, but it seems like every sport there’s a pattern. At kindergarten soccer league, we show up and Nehemiah scores half the points and dominates the game. Parents asked me if I have been playing with him, coaching him, what other leagues he has been in. I assure them that other than kicking the ball around with friends, we have not. This is just what he does. He is coordinated beyond his years. We show up to rookie baseball- the league above t ball. I wasn’t organized enough to get him into the t-ball league last spring. He plays baseball with the neighborhood kids, I think we’ve played catch a few times, but he shows up, has a swing like he’s in the MLB and hits into the outfield every. single. time. Parents gasp. The other 7 year olds back up when he goes up to hit. Coaches warn the kids to stay alert.

I have to say it is fun to watch. It also scares me. Our culture is obsessed with sports. It’s what’s cool in school- football will always trump math club. Though we pay professional sports players ridiculous amounts of money, 98% of people will be employed doing the tasks that are not cool in school. There are plenty of parents who are drilling their kids, forcing them into repetitive tasks too early in their development, thinking they are going to be the next Tiger Woods. I also don’t know if this ability of his is just normal physical development on an abbreviated pace. I’m already starting to prepare him that he may have great ability now, but this may all even out by high school. What I don’t want is sports to be the focus of his life and that will be no easy challenge. Unlike most of the toddlers at his daycare and pre-school classmates, I didn’t have him signed up for activities outside of school. It was easy to opt out of activities when he was oblivious. I am now allowing him to do one spring sport and one fall sport. Limitations will harder as he gets older. In the mean time, it’s his God-given ability and it’s fun!