Vaccination Craze

I am currently planning a wedding and among other things it involves the fears of my Southern family traveling to California. Some of it I was expecting, but when my mom asked if she needed to get a measles vaccination, I was pretty surprised. Indeed, coming to the Bay Area specifically right now may be pretty scary given the news on measles being everywhere. Although, I am glad the measles parties turned out to be a hoax.

I also have some postdoc friends with children under 1 years of age who are constantly terrified that their kids are going to get exposed here, so it's not a threat to be taken lightly. I am just glad I don't have any young kids. I do find that I am very frustrated by the many years of vaccine use and near eradication of major diseases that are now being undone by very ignorant parents.

I personally feel vaccination for lethal diseases, such as the measles, should be mandatory, except in immune compromised children. I experienced mandatory vaccine implementation firsthand when I traveled to Peru in 2012. In doing so, I was required to get a series of shots including Typhoid, Hepatitis A, Chicken Pox (I never had it growing up and it is required for SA travel) and Yellow Fever. I'm very grateful I did this in the states, because while taking a bus from Cusco to Puerto Maldonado (part of the Amazon basin), our bus was boarded by health officials checking yellow health cards for proof of yellow fever vaccination. For those without proof of vaccination, they had a small ice chest packed with syringes. It was a bit surreal to be honest and certainly not how I think 'mandatory' vaccinations should be carried out in the US. Nonetheless, it seems to be a strategy that is working in that Yellow Fever is much less prevalent in that area since its implementation.

In the mean time, I am not sure what to tell my family and friends as they prepare to travel to the Bay Area for my wedding. Although I take the situation seriously (I don't find it funny that kids are dying from going to Disneyland!), I do find it amusing/scary that anyone needs to consider getting vaccinated for travel within the US.

Why do folks only make resolutions at New Year's?

I have always been vehemently opposed to making New Year's resolutions mostly because it seems like an arbitrary time to focus on self-improvement. I've always maintained the mindset that you should constantly find new ways to make yourself better and make resolutions throughout the year to incorporate those changes into your life.

However, 2014 was a particularly challenging year for me and reminds me of my own 14th year in life. I guess the age of 14 whether it applies to yourself or your current millennium is a hard one. I saw on Facebook, many of my friends shared the same sentiment towards 2014, and I'm sure it can be agreed that 1914 was a pretty bad year as well. In fact, there are several similarities between the two years a century apart, including the reemergence of polio. Thus, with my energy drained from these challenges, I see the new year as an opportunity to wipe away the stains from those challenges and start new. With that my resolution for 2015 is to keep a more positive outlook by letting go of negativity more easily and not carry the weight of challenges and failures with me so much.

So basically, I've learned something I will likely learn again later in life - that principles I once held to strongly don't always apply to my current situation. This doesn't make me a hypocrite or anything, but time has changed my opinion... and it will probably change again later.

How food documentaries have changed the way I eat and think

Moving to San Francisco and getting out of graduate school have really opened my eyes to what I eat and prioritizing my health. I grew up in the south and despite having a mom who grew up on a farm, 'eating your vegetables' still means mostly canned food that has been cooked to the point of having very little nutritive value. Obviously, this means they had very little appeal to me. Honestly, it wasn't until I was on a trip to Peru and my friend force fed me fruits/veggies to help 'keep me regular' that I realized why they are an important part of one's diet. This was a much better argument than my mom's argument that they'd make my eyelashes grow longer. I've never once cared about the length of my eyelashes! In fact on a recent visit to family, I was eating some baby carrots and made fun of for 'eating rabbit food'. I think that made me realize that my family's notion of a healthy diet and mine were dramatically different. This is in part due to several food documentaries I've watched over the last few years that have changed the way I eat and think about food.

The first food documentary I watched was recommended by my fiance.  We watched the documentary Fat, Sick and Nearly Dead on Netflix, which opened my eyes to juicing. This follows the journey of an Australian man as he travels the US and completes a 90 day juice fast. He has been on immune suppressants for an autoimmune disorder related to his horrible diet. We immediately had my mom send us her unused juicer and started juicing. I'm sure my body was in total shock. Of course, like any busy couple, we eventually fell out of habit in juicing. Later, we watched the documentary Forks over Knives, also free on Netflix (we like documentaries!). I really liked this one because it wasn't as much anecdotal evidence so much as hard numbers and statistics. It really plays up the importance of a meat-based versus plant-based diet and the incidence of certain diseases and health problems. So, of course we tried having less meat-based protein in our diets. But, since I was born in Texas, I can never grow out of loving a good steak every once and a while! I can say that this transition was easier to stick to now that I had made an effort to have a serving of fruits or veggies with every meal.

Recently, we watched the documentary Fed Up (can rent from Netflix). This was by far my favorite. It gives a historical perspective on the battle between big food companies and health legislation, really highlighting how corrupt our government is. Most shocking to me was the unfamiliar landscape of children's cafeterias which resemble a fast food restaurant. I remember in high school when my school was 'sponsored' by Coca Cola and we got our first coke machines. I can only imagined how terrified I would be as a parent if my child's options for a 'healthy' lunch included pizza and hamburgers. So, of course, now we are working hard to pay attention to our sugar intake. We'll see how long it lasts, but I have noticed I feel much better overall. I don't even have that much of a sweet tooth, but this transition was especially hard for me. I never really noticed how much sugar I take in on a regular basis.

One thing that struck me about all of these movies is that they focus on the individual rather than how we can change society to help combat these health ailments that are plaguing our country. Living in SF, I have seen two major pieces of food legislation go up for a vote only to be voted down. One was the labeling of GMO's and the other was the recent soda tax. I voted against both of these. For GMO's I feel we'd basically have to label everything and that there is really no harm from eating GMO food. As for the soda tax, I feel strongly that the consumer should not be punished for consuming high-sugar beverages when our government is too weak to fight big food corporations who advertise to kids and are unwilling to admit the serious health risks they are imposing on our society. It is ironic when you realize that we as a country spend an exorbitant amount of our budget on defense, yet we are unable to defend ourselves against corporations. One piece of legislation I would like to see, which was mentioned in Fed Up, is to add a percent daily recommendation for sugar on nutrition labels. The recommended daily dose of sugar is 24-36 grams. However, many items in your local grocery store nearly reach that in a single serving, including soda. Adding 100% next to that 30 grams of sugar on your can of soda would help parents who are desperately trying to keep away unhealthy food options from their children.

Interstellar and women in science - warning spoilers!

I saw the new blockbuster Interstellar this weekend. I didn't really care for the talk of love transcending time and space, all the 'them' talk, and a bit of scientific errors discussed elsewhere. Other than these small flaws, I really liked the movie overall and even more I loved the treatment of women in science in this movie, and I'm not the only one!

In #Interstellar: Of the leading characters (all of whom are scientists or engineers) half are women. Just an FYI.

— Neil deGrasse Tyson (@neiltyson) November 10, 2014

The movie starts out with this ex-pilot Cooper stuck in the life of a farmer who gets a life altering opportunity to go pilot a mission outside our solar system and save the world. His young daughter he left behind eventually trains under the mission supervisor and basically becomes a physicist. Murph and Brand work together to solve the problem of relativity and eventually, as with any training relationship, she outgrows him and realizes his shortcomings. She then becomes the focal point of the movie and she ultimately saves the world! I LOVED this twist! Looking back, you realize that the movie starts and ends based on her timeline, not his. What's more, the narration throughout told through clips of elderly people, includes the old Murph we see at the end of the movie. She is really the central character, not her dad. This fact becomes obvious when Cooper returns and finds the space station named 'Cooper'. He seems honored for a moment and remarks that it is named after him. The guide quickly corrects him - the station has been named in honor of his daughter!

Are multivitamins really THAT bad?

There has been a recent backlash against the use of multi-vitamins in America. Several of the arguments make sense, but I'm afraid that with provocative titles like "Don't take your vitamins" and "Stop Wasting Money on ... Supplements" this backlash will actually lead to people who could use a daily multi-vitamin or with legitimate vitamin deficiencies becoming convinced that their pills are just a waste of money. Below are some arguments against multi-vitamins and other supplements and my criticism of these arguments. It's just my two cents and I suggest before giving up on anything based on a couple of harsh articles, do your own research on the topic and do what works for you!

1) Vitamins don't actually improve your chances of not getting cancer, dementia or heart disease. While there is a scary number of youtube videos with stories of warding of cancer with specific supplements of certain vitamins, I highly doubt anyone gives their kids the standard Flintstone multi-vitamins to ward off cancer, dementia or heart disease? In fact, the average American takes daily multi-vitamins to keep their energy levels high and to help them feel healthy. Yes, it would be nice if this actually led to staying healthy, but cancer is VERY complex and a daily vitamin or even a specific supplement will not be enough to alleviate a genetic predisposition to cancer. That being said, several of these studies go on to say that there are exceptions to this, specifically in calcium supplements, Vitamin D supplements, and in people at risk for vitamin deficiencies, such as patients with celiac disease or during pregnancy. One common deficiency in the US is Vitamin D, especially since sun absorption is blocked by sunscreen with deficiency linked to several diseases, such as Dementia. I personally have a diagnosed Vitamin D deficiency (doesn't hurt that I live in San Francisco!) as do several members of my family and I can report a remarkably improved energy level since supplementing. If I get cancer later in life, I won't attribute it to cutting back on my vitamin D!

I agree that the lack of evidence of multivitamins combating cancer, stroke, heart disease and dementia is compelling. But, this argument does not apply to some individual supplements or to patients who have a diagnosed deficiency. Also, several supplements have strong scientific evidence of being useful, such as folic acid during pregnancy, and calcium for women over 50 or those with osteoporosis.

2) Vitamins have quantities that are so large that they are a complete waste and sometimes lead to overdosing, or in the words of Sheldon Cooper, expensive urine! This is a point I agree with, partially. With the individual content of certain nutrients in multivitamins being so high, you end up peeing the contents out within 30 minutes. That definitely doesn't feel like money well spent. In fact, there are several problems with high quantities of individual vitamins in multivitamins. First, your body can only absorb so many vitamins and minerals in one sitting. For example, you can only absorb half of your daily calcium intake at a time, which is why when taking independent supplements, you take it twice a day. In a multivitamin with 2-3 times your recommended daily allowance, the remaining bits will be filtered out by your kidneys (hence the iridescent urine!). Second, there is the issue of overdosing. While there is very little evidence that you can OD on Vitamin C or B12, it may be an issue for iron, beta carotene, and folic acid. Third, there is the problem that the multi-vitamin approach includes vitamins that inhibit each others uptake, such as calcium, iron, and zinc, which should not be taken together, reducing the overall effectiveness of the multivitamin.

My answer to these problems has been to switch from pill to gummy multivitamins. I find that gummies are easier for me to take because I hate swallowing pills. Though, I find gummies typically have less than 100% of you daily dose for several vitamins and even lacks some, such as iron. I also have added individual supplements for vitamins such as calcium and vitamin D. For the calcium it allows me to get closer to the full recommended dose by taking it twice a day (though if you split you multivitamin dose you might be fine) and for the vitamin D it gives me above the recommended dose because of my deficiency. If you don't want to take your vitamins like a child, you can split your dose in half and take it twice a day.

3) Money is better spent on fruit, vegetables and exercise - all shown to have better impact on your health. I agree, but the evidence actually shows that most people who are conscientious enough to take daily vitamins generally have healthier lifestyles. They are not taking them because it's easier than going to the gym, as some articles suggest. It is more like an "insurance policy against an imperfect diet" explains Dr. Oz, who also disagrees with the harsh multivitamin criticism (though that doesn't mean we agree on everything!). I personally try to get 2-3 daily doses of fruits and veggies, but I can honestly say after tracking my healthy diet for several months, I never got above 50% of my required iron and calcium intake. In my case, I am lactose intolerant which explains the difficulty getting enough calcium. Though, I have recently found a bowl of cereal with Almond milk to solve this problem. However, the iron from cereal may not be as digestible as we have been led to believe. In fact iron supplements warn against calcium intake within 2 hours as it reduces the absorption of iron, meaning cereal is probably the worst food to iron fortify! Nonetheless, given the average monthly cost of vitamins can range from $20-$50, I would say a gym membership and a weekly trip to the farmer's market would be a better investment if that isn't already part of your lifestyle. In fact for some vitamins such as Vitamin E, food absorption is much higher.

Bottom line: Do your own research and reach your own conclusion. But don't throw out your bottles of multivitamins just yet and certainly don't use it as a replacement for a healthy lifestyle! And buyer beware - it won't cure cancer!

Basic shell navigation and trouble shooting

Here are some basic tips for navigating the shell that a biologist, like myself, may not know if you're just picking things up as you go. Some can save you a lot of time and/or a lot of frustration! For more see: A Command Line Primer for Beginners.

1. Personalize your bash_profile/bashrc.

   -Ls colors is a nice option to highlight executables, compressed files, directories, etc. This can save time for example if you spent all afternoon troubleshooting a program only to later realize it is not executable. It's also a quick way to see which files you can compress to reduce your quota on a server. See here for more on LS colors.

   -Add aliases to your bash profile to save time; can include shortcuts to directories, ssh shortcuts, and common commands (especially if you are attached to certain command options). Other tips for customizing your command prompt are here.

2. The power of less: I prefer less over more because it doesn't clutter up my terminal. It also only loads a page at a time, so for large files, it's nice to get a peak without having to open the whole thing up. You can also search within less, which may be faster than grep if you aren't sure what you are looking for. For more tips, try here or check the man page.

    -'/' and '?' allows you to search forward and backwards within a file

    -'g' and 'G' allow you to scroll to the beginning and end of a given file

   -'shift+F' allows you to turn on live streaming in a file that is currently being written

       note: alternative is tail -f, but this output will stay in your terminal afterwards

    -'-N+enter' adds line numbers

    -'###+g' scrolls to a specific line number in a file

3. Shortcuts on the command line. I've seen so many friends mistype on the command prompt and painstakingly back type the entire line. Below are few shortcuts to avoid this frustration, but for more check out: Keyboard Shortcuts for Bash.

Ctrl+a moves to beginning of the prompt
Ctrl+e moves to the end

Ctrl+k erases everything after the cursor

Ctrl+u erases everything before the cursor

Tab to autocomplete filenames from within your path

4. Quick and useful one-liners. Lots of times I do very simple text manipulation that a simple one-liner can do efficiently as compared to a separate script. The nice thing about performing these tasks on the command line is that it makes it easier to employ piping the output from one into the next to avoid lots of intermediate files, that later avoid deletion or archiving. 

Get column sum or average quickly using awk:

$ awk '{sum+=$4} END {print $4/NR}' somefile #calculates average across column 4 (remove '/NR' to get only the sum of column 4)

Add header to file using sed (-i option edits files in place):

$ sed -i '1s/^/header\n/' somefile #add header or other text before the first line of somefile

Convert file with chr1 to 1 or vice versa (useful for switching from UCSC to Ensembl files):
$ sed -i 's/chr//g' OR sed -i 's/^/chr/g'

Count the number of fasta entries in a fasta file (more grep tips):
$ grep "<" infile.fasta | wc -l

Convert line endings from MAC to unix/linux:

$ cat macinput.txt | tr "\r" "\n" > unixoutput.txt

Quickly check the syntax of your script without running it:

$ perl -wc script.pl

$ python -m py_compile script.py

Find a lost file (searches within current directory and all subdirectories), more find stuff:

$ find ./ -name somelostfile.txt   

Change something across multiple files:

$ find ./ -name "REGEX" -print | xargs sed -i 's/old/new/g'

More one-liners can be found here: Useful linux one-liners for bioinformatics. Also, I use awk and sed a lot and for loops in bash are pretty useful. This list is by no means comprehensive, but it's a great start! Feel free to add any additional tips or links in the comments!

Advice for making the transition to the postdoc stage

After the dissertation you are on a high from the massive accomplishment you've just done. Then you start your postdoc. You are surrounded by new people who have no idea who you are or what you are capable of and for that reason you may find yourself feeling like a first year grad student all over again, trying to prove yourself and feeling strangely like an impostor despite your newly minted PhD title. This feeling may even have started when you first began looking for postdoc advisors and were intimidated by professors who had no idea who you were. Here are some tips to help you cope:

(1) You're still in training! - Remind yourself that you are capable and you have a PhD, but you are still in training and it's okay to admit when you don't know something and need help. I'm sure you've helped a fellow postdoc in your former lab as a grad student, so look to grad students in your current lab as they are likely the experts on new protocols and such. It's more than likely you'll go through a second round of impostor syndrome (assuming your first was in grad school), but know there is support. On Valerie Young's site, you can sign up for weekly 'impostor buster' words of wisdom to remind you you're not alone and you can do it!

(2) Seek out teaching/mentoring opportunities - As a former senior grad student in a lab, you may be used to having people solicit you for help. Though this may have been taxing on your time, it comes with a sense of authority and know how that maybe you are lacking as the new resident 'knowledge sponge' of the group. You should seek out opportunities to mentor and/or teach as a postdoc. This will help boost your morale and beef up the CV in preparation for job applications (should that be your ultimate route). Volunteer for a guest lecture here and there to keep your teaching current and to reinforce the stuff you're learning in your postdoc.

(3) Don't let yourself stay isolated - Even in a large lab or department, a postdoc experience may differ drastically from a grad student experience where you start with a large group of incoming students from different labs and your academic committee forces you to interact with other PIs. It is important to find a group of folks either at your university or elsewhere that you can meet with regularly for emotional and scientific support. If you need help defining or organizing such a group, see: Every Other Thursday for how this model has succeeded for women in science for decades.

(4) Keep up with the literature related to you dissertation work as well as your postdoc - After my first year as a postdoc, I attended a specialized meeting in my research area and realized I had lost touch a bit with the literature in just a year being surrounded by folks in a new area. Upon discussing this with another fellow postdoc finishing up her first year as a postdoc, we decided to organize a virtual journal club for just the two of us via skype. This has been GREAT and grown in the last few years to now include ~5 people. I highly recommend it as a way to keep up with the literature while undergoing new training. It can also satisfy #3 above as a group that helps you from feeling isolated (but a local group always helps).

(5) Get out there and make a name for yourself - You're a postdoc now and an increased level of independence is expected of you. Be proactive about making a name for yourself as a scientist. Some suggestions:

Take to the web: get on twitter (this can help with #3), build a website, or start a blog!
Be active at meetings: volunteer to chair a session or to mentor an undergrad or grad student
Get invited to give talks: ask friends to invite you to their universities to give a talk or invite yourself to nearby universities to talk so that folks in your area know who you are

(6) Have fun! This is the stage where there is the least amount of oversight on you - no committee meetings, no real requirements of you at all. You aren't a professor yet, so you don't have to teach or be on any university committees. You just get to do science! Although this sounds freeing, it is also just enough rope to help you lose sight of your goals - don't let that happen. Stay connected to the field and avoid going deep into academic purgatory!