Bat by Bat- writing as a biologist

Writing can be tough.  It can frustrate, madden or bore- but it is also rewarding.
This is the topic of today's post.

Much of being in academia is writing and scientific writing can be particularly intimidating.  It is commonly jargon rich, feels non-creative and highly formulaic.  This is because for a paper to be successful precision and thoroughness are key while creativity or prose tends to be an afterthought.

In any case, I find that writing is a key aspect of my work-life I most wish to improve upon or at least enjoy more.  Thus, I'm always excited to learn about books or other resources about writing, presenting motivation or even better advice on how to be a more efficient writer.  For example Stanford has a series of videos that present interviews with different faculty members - each discussing why writing matters to them.  Below is the video from Deborah Gordon a well-known biologist who studies ant behavior and has written several books on this topic.

My favorite part of the video is when she says:  

"when someone really understands what then mean to say- 

they don't need jargon anymore."  

I very much agree with this idea.  Even in scientific papers where researchers explain complex methodologies, results and concepts I believe they should be able to at the very least write a jargon free abstract AND discussion.  I often describe this as the 'explain it to your grandmother requisite'.  Namely, one should be able to explain the ideas and general methods of what they are doing research-wise to anyone- particularly grandmothers.  (I choose to think of explaining it to a grandmother because in my experience they are so often: interested, patient and encouraging- in my mind - the perfect audience)!

Perhaps in science we want others to think we are smart so less weight is put on this skill: communicating clearly without jargon- whereas obtuse writing is rewarded because if it is difficult to understand 'you must be smarter than I am'.  This is just a guess.  In any case, it seems to me to be a rather unfortunate state of affairs.  Particularly sad and surprising is that early biologists did not always write in this way.  Pick up early papers by Darwin for example, and I think you'd agree that things are presented in a much more story-telling manner.

So while it is most certainly not a book aimed at non-fiction writers I ordered a copy of the book Bird by Bird.  It arrived today and I am so excited I may spend the rest of the night reading it!  Bird by Bird is written by Anne Lammot and seems to be funny and inspirational.  I learned about this book from another blog: Orangette- where the blog's author: Molly spoke very highly of it and I get the impression drew a good deal of inspiration when writing her 2nd (no I haven't bought it yet- but I will....) book.

In any case Molly is a great writer and makes me smile a lot with her blog posts so I tend to take her word not only on recipes (hasn't let me down yet) but on writing as well.


"I had the strangest feeling. It took me a long time to figure out what it was, because I’d never felt it before. Turns out, I missed writing.  ... I know that probably seems like a perfectly normal thing to feel, given that writing is what I do. But the truth is, most of the time, I will do anything to avoid it.
...
I understand that some people wake up itching to write. They feel as though they somehow aren’t complete unless they’re writing. I have never been one of those people. I have wondered what it’s like to be one of those people. Sometimes I have wondered what it would be like to punch those people."

 She also recommends this lovely Ted talk by Elizabeth Gilbert which I will echo here- it really is great!

Bird by bird's book description is pasted here from Amazon:  (Book Description)

Release date: September 1, 1995 | ISBN-10: 0385480016 | ISBN-13: 978-0385480017 | Edition: 1

"Thirty years ago my older brother, who was ten years old at the time, was trying to get a report on birds written that he'd had three months to write. It was due the next day. We were out at our family cabin in Bolinas, and he was at the kitchen table close to tears, surrounded by binder paper and pencils and unopened books on birds, immobilized by the hugeness of the task ahead. Then my father sat down beside him, put his arm around my  brother's shoulder, and said, 'Bird by bird, buddy.  Just take it bird by bird.'"

Anyway- hopefully I've given you some useful links here and inspired you to think about how scientists do and should write.  I am not going to launch into the whole 'Publish or Perish' dogma in academia.  Perhaps another day.  Plus- really the fact of the matter is that I think there are much more positive ways to view the publishing process.  So as I work my way through this book and try to find my own muse- I'll share more about that here!  Meanwhile it is bat by bat for me!

So now... not much to do but get to it!

Fractals inception-style and the father of fractals: Benoit Mandlebrot

I am currently reading Chaos Making A New Science by James Gleick and my mind seems to be lost in a perceptual run-through of the beauty of fractals.  The term fractal was coined by the amazing Benoit Mandelbrot.  Here I refer to his science but it is worth mentioning that he lived a very fascinating life including escaping Nazi persecution upon fleeing his native Poland to France and thus the science he was able to conduct in his life is all that much more precious.


His research and 'knack' for seeing fractals has resulted in him remaining one of the most inspirational scientists I can think of.  I am not alone in this thought; James Gleick in Chaos himself says:

"Benoit Mandelbrot was the one who let us appreciate chaos in all its glory—the noisy, the wayward, and the freakish, from the very small to the very large. He invented a new and slightly nebulous field of study—a kind of geometry, for want of a better description—and he invented that recondite name for it, fractal.^"

Certainly a 'character' I highly recommend his TED talk (below).

 

"The beauty of geometry is that it is a language of extraordinary subtlety 

that serves many purposes".   B. Mandelbrot

So what is a fractal? 

Fractal is a word introduced by Mandelbrot to describe a mathematical concept also witnessed in the natural world of self-similarity across scales.  (Inception style!)   

An example of this can be seen below in a loop continually zooming in on a a Mandelbrot Set image across scales.  You see the shape (large circle on right attached to a small circle on the left) but as you zoom in you see that this shape is made by many smaller versions of the same shape.  Zoom in on any one of those and you will see a smaller self-similar FRACTAL of the original shape and so on.  Repeat as long as your brain can tolerate the fractalness!  Me?  My mind is already blown by about 3 fractals!  ;)

Fractals are mathematically non-differentiable.  Needless to say mathematically-speaking fractals are quite complex and I am not a mathematician so I will instead focus on a few cool examples. 

Fractals in nature:

An example of fractals in nature- broccoli.

Mountains- fractal.

The airways of a mammalian (dog) lung.  From: Dr. Robert Henry DMV of the University of Tennessee College of Veterinary Medicine via:  http://classes.yale.edu/fractals/panorama/biology/physiology/animallungs/animallungs.html

Finally- to me feathers are also fractals- but I could be wrong (what do you think?)

Mandlebrot ran computer simulations of complex numbers in mathematical operations approaching infinity to reveal the patterns of fractals that result.  In addition to the resulting images that are the poster-children of Fractal research (examples above and below)- he published several books with lovely fractal images.

In his famous paper written and published in Science (1967) Mandlebrot clarifies the concept of the fractal further titled: "How Long Is the Coast of Britain? Statistical Self-Similarity and Fractional Dimension"

Here he presents a case where ... 

...say you were to measure the coast of Britain using a measuring instrument of the size indicated below you can imagine your work process and end result would look something like this:

 Now lets say you realize you've missed some little pieces of the coast (see there on the left-side?) so you decide to do this again but now with a smaller measuring implement.  Britain suddenly gets much larger (more coastline) (see below)!

 This process could be repeated again and again with a smaller measuring implement (see you still missed some bits of the coast) and you would find that the coast is still larger...still missed some?  Repeat- and boom!  The coastline is longer (and so on till you find yourself crawling along the coast measuring around pebbles and sand to get each contour of the coast!).

Why is the coast longer and longer - the finer scale you use to measure it?  Well the coastline is fractal and the closer you look the more curves/lines indents and whatnot it has. As you add these imperfections to your measurements your 'estimate' of the coastline with be longer, longer and LONGER!  Inception-style!

Ok- as this post is not really about bats I should stop digressing and get back to the bats!  

This has just been brief introduction to the lovely world of fractals and I hope you are now equally excited as I am about  fractals and the legacy of Mandlebrot.  Fractals seem to be a place where mathematicians, biologists, and artists can have many an inspiring exchange!

 

Note: What is 'inception style'?  

'Inception style' refers to a concept from the movie Inception (term coined by graduate students in the OEB program at UMass Amherst in conversational settings).  Inception was released in 2010, directed by Christopher Nolan and stars Leonardo DiCaprio.  I don't want to ruin it for you so I'll suggest you Netflix it or at least watch this trailer to see how Inception Style is another example of fractals!   

Ie. Fractals in Hollywood?  

 (Perhaps it only works if things get 'smaller' as you repeat (I'm being careful to not say too much and ruin it for you- but think on it if you have seen it))!

World War II's Other Secret Weapon- BAT BOMB

Believe it or not but during World War II plans were made and nearly successfully executed to attach tiny bombs onto bats. These bats would do what bats do- find nice areas to roost inside homes, with a catch, they had a bomb with them wherever they decided to call home. Because homes in Japan were made of wood and paper the idea was that bombs would destroy houses that were common throughout Japan.

Plans for what became called Project X-Ray was hatched by Donald Griffin, a Harvard scientist and famous bat researcher and a very young Jack Couffer among others.

An excellent and often funny book on the topic titled Bat Bomb by Jack Couffer tells the whole story. A famous bat named 'Flamethrower' is also discussed in the book. Flamethrower was a Mastiff bat (Eumops perotis) which is the largest bat that occurs in the US, weighing around 60 grams (~2 oz). Because the bombs that were designed for bats to carry needed to be small and light-weight Flamethrower who was tame was used as a model for various prototypes. The problem however was that Flamethrower as a Mastiff bat was much larger than the bats that were going to be used for Project X-Ray! Needless to say the project had so many problems (including unplanned bat-initiated explosions!) that it never went into action.