Sunday, December 30, 2012

Writing

It's unavoidable.  To be a successful scientist, you must be a good writer.

You don't have to start off being a perfect writer (improvements will come with practice), but you have to LIKE writing.  Enjoy sitting by yourself with the bum in the chair.  Be one with your computer.  Be an expert at picking out the perfect blend of music that is energizing without being distracting (or no music).  This is why scientists are such major coffee drinkers: it's not from all the lab and field work!  Think about the major term papers you wrote in college, and how much you had to focus on them, every day, for weeks at a time.  How you probably said "no" to social events and sleep to get it done.  This is the life of a principal investigator (PI)!

As a busy graduate student, wife, and mom, I find it very difficult to sit and focus on writing.  Field work keeps me busy, but when I choose field days and put them on the calendar, I just get it done (with a lot of help from my labmates).  Labwork is similar: you show up in the lab and just DO it.  Luckily, I have enough different components of my project that I always have a lot of different tasks to do in the lab, and I don't get bored.  Again, I have a lot of helpers and people I can talk to while I work.  At the end of the day, I go home.  But writing.... writing is a solitary enterprise.  It's just you.  Any failings are solely your responsibility.  It's daunting.  And kind of like managing a household, with writing, you're never finished.  There is always something to be tidied up, looked at again, re-organized.

I'm still early on in my writing "career", but my husband gave me an amazing Christmas gift this year: the gift of peace and quiet to write.  He sent me to my parents' house (on a plane!) with all my papers and computer and warm clothes, so that I can get my prospectus DONE.  Away from him, our children, his parents who are visiting, and all the responsibilities of planning activities for the family, cooking dinner, cleaning the house, laundry...  I set up a card table in my parents' living room, and they have been good about leaving me alone.  I haven't left, except to eat and sleep.  And I have been so productive!!  This is great news for the family because it means when I get home, I can relax and have fun with them on New Years' Eve without being grumpy and stressed, and still have a few days before the kids go back to school and I go back to work.  It seemed like an odd Christmas present, to send Mom away the day after Christmas... but Rob knows me so well.  He knows what I needed career-wise, and that it would have a good effect on the family as well (less stressed Mom).

The thing that worries me is that there will be a LOT more writing like this in my future, if I expect to continue in academic science.  I'm not always going to be able to sequester myself from my family and responsibilities in this way.  I'm going to have to find a way to focus on my writing, and somehow have it mesh with the rest of my life.  It's not fair to ask Rob to pick up the family slack every time I need to write a manuscript or proposal.  Somehow, he has found a way to focus on writing while sitting at his desk in our house, and he makes it work!  I am lucky that I have such a great model for scientific work ethic in my own home.

So, if you are considering a career in science, don't just think about those lab classes that you enjoyed, or field trips to the marsh or on the boat where you got to use cool equipment, make observations, and take data in your notebook.  Think about days and days, weeks and weeks, months and months with your bum in the seat, staring at a screen.  Get a reliable computer and a comfortable chair, lots of coffee, and the most willpower you can muster.

Friday, October 26, 2012

Game of Telephone

Remember the game as a kid, where everyone sits in a circle, then the first person thinks of a short phrase, and whispers it to the child next to him?  Each child in turn whispers the phrase he hears (or thinks he hears) so that no one can hear except the one being whispered to.  Usually by the time the phrase gets back to the beginning, it has significantly changed.

"I wish we could all go on a plane to Disney World" slowly changes to
"A fish swims on time to Disney World"....
and so on.  Before you know it, Disney World isn't even mentioned.

Why does that happen?  Is is because we are hard of hearing, or because we hear only what we want to hear?

This "broken telephone problem" is a rampant problem in the news media as well as in science.  People's background and view of the world affect how they receive information, and scientists are not immune.  Our background, training, and belief systems affect our presumably logical reasoning.  This is one reason why the scientific method is so important: it gives scientists a framework for formulating, testing, and evaluating hypotheses.  The peer review process is a related system of checks and balances that helps results of experiments become accepted knowledge through the repetition of experiments and evaluation by qualified colleagues.  Results become conclusions, which through repetition, become facts, and eventually theories.

Almost all current scientific writing draws on past scientific facts and theories to provide background for, justify, compare or contrast with the experiments being presented or proposed.  Scientists receiving funding support from a granting agency need to justify the necessity of the supported project and how it will advance scientific knowledge or provide answers to questions for the common good.  Justification of an idea can come through a clear and logical explanation, but most scientists use the results and conclusions of previously published research to justify similar research or conclusions.  The more scientific literature I read on a common topic, the more it reminds me of the law field, where lawyers or even Supreme Court justices use logic to evaluate a present situation and apply the conclusions of a similar decision from the past.

Thomas Kuhn, philosopher of science, coined the term "paradigm shift" (http://www.molwick.com/en/scientific-methods/041-scientific-methodology.html)

Drawing from the knowledge and conclusions of past research and building upon it is vitally important for the advancement of science, but this system will only work efficiently if the logical links between past and current research are accurate.  These logical links go something like this:

Past paper:  Hypothesis -> Test of hypothesis -> Results -> Conclusions (support/do not support hypothesis) ->
New paper (generally in introduction and/or discussion section):  Evaluation of past paper's hypothesis
-> Critique of whether methods were appropriate, results were reasonable, conclusions were supported by results -> Synthesis of past paper with other past papers -> Translation and application to new problem or the next step -> Justification for new research

That is a lot of logical links.  A lot of people in the game of telephone.  A lot of potential for broken wires.  There is even more potential for breakage when this process is sped up.

Ten or twenty years ago, the publishing process was faster and there were a lot fewer papers being published.  Therefore, the conclusions of one paper could be addressed reasonably by a similar study a year or two later, and there was some dialogue between scientists in the literature.  Even ten years ago when I started my MS degree and was writing my prospectus, I had to visit the library to photocopy the papers I looked up by title in a database, but I could copy and read the major papers on the topic in a day or two.  Over the course of my MS, I added maybe 5-10 papers to my thesis that were recent publications that had come out since my prospectus.  I had some time to assimilate the information I read, formulate my own research questions, conduct the experiments, and write up the results as they related to previous work in the field.  Now I am writing my prospectus for my PhD, and every time I search the literature (ahem, Google Scholar), there are 5-10 more papers for me to read.  Do I read them all?  No.  Could I possibly?  If I did nothing else, maybe!

What happens when scientists are overloaded with reading in the field, reading in related other fields, and sitting in front of Google Scholar with 30+ recent abstracts in front of them while they write the introduction to their paper?  Do they individually download, read, and evaluate each of these studies before drawing conclusions that can be addressed in their own manuscript?  What if there are some older "classic" papers in the field that should be acknowledged in the introduction, but that are not online?  What if your institution has gotten rid of most of its paper journal collection to save space, in favor of all electronic journal databases?  What if some of the papers needed are in a journal not supported by your institution's database?  Would you get an interlibrary loan for those 30+ papers?  Would you pay cash for the electronic version?

What if the papers you do have cite that older paper as evidence for the phenomenon you are looking to describe, but you can't find that older paper?

I'll tell you what many scientists do.  They cheat.  They either (1) ignore the difficult-to-find paper that keeps coming up in the database and look for a different paper to cite, (2) use just the abstract from the paper to draw a conclusion that is cited, or (3) use the secondary source (someone who cites the primary data collector) and either use the secondary source's reference, or misattribute the data to the secondary source rather than the primary source.

It seems like an innocent (though admittedly lazy) process, but it can result in real problems.  Exaggeration of conclusions, giving credit to the wrong authors, even completely getting it wrong by mis-reading or mis-quoting a sentence or two.  But is this really cheating?  Is it lying?  Is it misconduct?  Probably not in the same way as falsifying data or plagiarism, but it does cause similar problems in the scientific process.  It causes erosion and breaks in the logical chain that advances scientific knowledge.  It causes paradigms to be created that are not supported by reason.  It causes misunderstanding and mistrust of science by the general public.  It can result in policy decisions based upon consensus belief rather than data.

My husband, Rob Condon, is working on a paper with colleagues addressing the "broken telephone" phenomenon as it applies to the paradigm of jellyfish blooms increasing worldwide.  The belief in this paradigm by the public as well as the scientific community is astounding, considering the lack (so far) of scientific data on the subject.

Some other students and I have been getting frustrated at the number of broken logical links and misattribution (AKA "citation trail") we have been finding during our literature searches, so we have been talking about starting a published list of the broken telephone offenders that we find.  Maybe it will bring a little more recognition to the topic.

In conclusion:
- Don't be lazy
- Go ahead and skim the abstracts, but if you're putting something in your paper, make sure you've read it thoroughly
- Remember that the author you are citing might very well be your reviewer
- (On the other hand) Many, many papers play the broken telephone game and make mistakes, and the only way to keep from magnifying this misinformation is by going to the original source and evaluating their data and their conclusions for yourself
- Getting caught would be really embarrassing and you don't want to end up on our List of Broken Telephone Shame.

I would like to acknowledge my advisor Ruth Carmichael for encouraging lively discussion on this topic in her Scientific Communication course, and Kelly Robinson for her Facebook status update inspiring me to finally write something about this pet peeve!

Please submit examples of misattribution, misquotation, exaggeration, and other breaks in the scientific telephone line in the comments below!  The more specific you are, the better.  Thanks!

Tuesday, October 2, 2012

Naked Science

5 am, Rob is on a Skype conference with 4 international collaborators in the kitchen. Tristan wakes up and goes down to see Daddy. I hear T get up and go down in my PJs to get him. Then T realizes he is wet, and starts crying and trying to get his wet PJs off, in the bathroom directly behind Rob and in the line of vision of the camera. So before you know it, Rob's pajama-clad scientist wife and half-naked son are displayed on screens in Spain, Australia, and England simultaneously. Hi, Carlos Duarte!

Sunday, September 30, 2012

Wanting to Love Math and Computing

I love science, but it doesn't necessarily come naturally for me.  The logic part usually makes sense, the scientific method was an easy fit, and I never really had trouble memorizing long lists of biology vocabulary words.  But despite my chosen career being Science, I still have problem with the "Math and..." part of this field.  I keep hoping that, like chemistry, the more I force myself to do math, the easier it will get.

In eighth grade, I knew I wanted to be a marine biologist, even though I was always better with words than numbers.  After taking Life Science in 7th grade and going to a summer marine biology camp (marsh mud!), I was hooked.  I tested for the county magnet high school for math and science, and did not get in (hmmm... maybe the MATH part??).  I went to a good high school and had some great teachers who encouraged me (hi, Mr. Mensh!), and forced myself to take advanced track math and AP science courses.  Oh, the math.  From algebra onwards, I struggled.  Geometry and Trigonometry were OK.  Pre-calculus and Calculus, I struggled some more.  My dad tried to help me, my boyfriend tried to help me, I cried, and I dragged myself through it.  I managed to get by with OK grades, but I had to work.  But I still didn't get why I would need to be so good at math to have a career in science, because so far, the most math I needed in high school science classes was a little bit of algebra.  I did great in my science classes without much math acuity.

Meanwhile, that mathy boyfriend of mine was getting into gaming and writing computer programs with his guy friends, which to me seemed pointless (unless you wanted to be a software developer or have a startup and make lots of money, which some of his friends were already doing).  It wasn't relevant to my chosen science career.

In college, I took one calculus class (which was pretty much a review of AP Calculus I took in high school) and one intro to statistics class to fulfill my math requirements.  The science classes I struggled the most with were organic chemistry and genetics, and this had nothing to do with math (more like the amount of memorization needed for all the classes to complete my double major conflicted with my social life).

Even in my masters' program, I took the required courses (including statistics and some physical/geological courses that used a little math), completed my thesis, and probably used calculus all of about 3 times.  Then I worked for a biological modeler, and he did all the math.  But I started seeing how really useful it could be.

If I can master these mathematical functions, and get them into computer code, there is so much I could do.  I could use my files and files of data to start describing biological and physical phenomena as a pattern, and compare this to other patterns, in really elegant ways.  I could predict future results.  I could write papers without doing experiments.  I could do virtual experiments!  I wouldn't be limited by existing statistics packages that charge a lot of money and never quite do what I want them to do.  I WOULD BE ALL-POWERFUL!  BWAH HAH HAH HAAAAHHHHH!

Now I'm starting to sound like that high school boyfriend.

So, now that I'm doing a PhD and am hopefully going to be an academic, I need to up my skill level and challenge myself.  I've been hearing people talk about the language R for a while, and when a fellow student passed along the link for a free online course starting last week, I thought I would check it out.  I had looked at R before, but it didn't seem very intuitive, and I never had time to play around with it.  I didn't think I would ever teach it to myself, and no one is teaching it at our institution.  So I signed up for the course, which is through Coursera and Johns Hopkins School of Public Health.  Apparently 40,000 people signed up.  It's a 4-week course, with video lectures and online quizzes and assignments.  I feel pretty lost, but I am working really hard at it, because I've seen how powerful R can be.  I want to be that girl who can type up a command in R and make a pretty graph, or call a function with a few commands at the drop of a hat.  The only remotely similar experience I have with a computer language is with SAS, and that was a long time ago.  R is hard.  Or maybe this course is making it hard.  But once again, I feel like I am struggling the way I struggled in high school with calculus.  I am trying to hard to recognize patterns (didn't I say I was good at logic?  Not so sure anymore!), and spending probably 10x longer with it than most people taking this course.

I'm thinking that stretching my brain in this way is good for me, like doing crossword puzzles or Sudoku, so I will be less likely to get Alzheimer's.  In the meantime, I am tired, and honestly, find Facebook and blogging much more interesting!

Monday, January 30, 2012

Scientists Living Apart

Rob got back from his work trip to Australia a few hours early yesterday, which was so exciting for us because it meant the boys got to see him before they went to bed.  It was an exhausting, long trip for him, but it was so good to see him because (a) I love him very much and missed him and (b) the boys love him very much and missed him and (c) it just makes life so much easier when he's around.  I realize when he's away that I rely on him so much, and I am much more organized and on top of things when he is gone.  It's because he's so capable at taking care of the kids and the house, doing the daily routines, and even (usually) staying on top of calendars and dates and school stuff, that I get a sense of complacency when he is here.  We don't sit down and communicate as much as we should, so things are actually probably less organized when he is around.  1+1 does not equal 2, because we both assume the other is doing things that we aren't, necessarily!  Time also flies by when he is here.  I am content to just spend time with him, even if it's doing mundane things.  But then later I will wonder where the time went.  Did we really just spend a whole weekend driving around and looking at rugs, but didn't buy anything??  I am happy just to be with him and the boys, and to have a little break from our hectic weekly schedule.  I'm sure the boys don't love driving around looking at rugs all weekend.  I also really missed having him around to talk to.  I guess I don't really have friends.  I mean, I have my old, lifelong friends, who would love to hear from me, but I usually don't have the energy for a long conversation.  I have lab friends and church friends who I chat with when I see them, and who could help me out in a pinch if I needed someone to help pick the boys up.  But I don't have those local friends that I could just go grab lunch with, go shopping with, get my nails done with, and just vent.  To tell stories about the sweet old shrimper I met at the auction, or the two dented chemical cabinets that were delivered to our lab within a week of each other.  These are things that Rob doesn't particularly care about, so I don't feel the need to tell him about in our 20 min Skype conversations.  But they are the things I tell him about when we are driving together, cooking together, just going through life together.  He travels a lot for work, and this is part of being a marine scientist.  I travel a good amount too, but he has projects in Bermuda and Santa Barbara and recently, this trip was an all-expenses paid opportunity to collaborate with one of the gurus of marine science.  In Perth.  Ugh.  This weekend when I was getting organized, I looked at the calendar for February and realized he is leaving again for Santa Barbara in less than 2 weeks.  Then he goes to Bermuda in March.  And again in July.  When we were driving to lunch today, he was telling me about a conference that's going to be in Japan next year, and how it's close in time to another conference in Australia.  I know what he's thinking - joint trip to Japan in Australia.  And I know what it will mean: 2-3 weeks of him on the other end of the Earth.  I told him he travels too much and he was quiet after that.

When we decided to leave Bermuda to pursue our careers back in the States, it was a very quick decision, and Rob had to leave Bermuda right away to get started in Alabama.  It was May, and I needed to stay until the end of June so that Ian could finish kindergarten, and to give myself some time to get our stuff packed and us moved.  International moves are no picnic.  So it was 6 weeks of living apart from Rob, plus the added stress of the move and finishing my job and transitioning to another, plus daily life with a then 5-year-old and 2-year-old.  My mom came to help for 2 weeks, which was awesome.  But mainly, I just really missed Rob.  It stressed me out so much to be away from him for that long.  It was hard on the kids.  Plus we had the added emotions of leaving friends and the beautiful island we had come to love.  But mostly, I missed Rob, and hated having our family divided.  I think ever since that time, it has been really hard for me to be apart from him.  I know that I could never live apart from my family for any extended period of time (some scientists do this temporarily while they are starting new jobs or finishing another).  I would rather sacrifice my own job possibilities and take a different job (even if not in my field) just to be in the same geographic location as my family.  And over time, I would get frustrated that my career was being stunted, but it would take me a while to come to this conclusion (for example, Bermuda).  :)  And we would find a way to make it work, together.

Tuesday, January 24, 2012

Prospectus...

How much do I love these editing comments?

"I'm not sure I agree with your objectives" (on the third draft)
"Needs some kind of transition...."
"Needs a little more explanation."
"?"

My favorite editing comments:
The ones where things are crossed out and replaced by what they really should be.  Thank you, that is helpful.  :)