Back from Vacation

An afternoon in Tuscany

Last month I went to the Single Molecule Approaches to Biology GRC in Italy and had a wonderful time meeting delightful people and learning about cool developments in the field. It was a pretty great week. GRCs don't allow recording of the scientific sessions, but I was allowed to snap a few photos of the gorgeous view from the hotel.

After the conference, my husband and I spent a couple weeks vacationing in Italy and Germany, seeing sights, eating delicious food (we had the best gnocchi in Florence), and visiting old friends of mine. We came home happily tired from all the travel.

After that, I took a sort of technology vacation. It was unintentional to begin with: I had almost gotten used to being Internet-less. But after a few more days, it was really nice not to feel the pressure of email and Facebook and the endless stream of Twitter. That was as relaxing as anything else after we came home.

But I have a new job, and even if it doesn't start until next week, there is preparation to do already. So this week I reconnected myself to the buzzing web. Blogging will resume shortly.

Book Review: Culinary Reactions

The Book

Culinary Reactions: The Everyday Chemistry of Cooking by Simon Quellen Field

The Premise

This books purports to explain the hows and whys of cooking in terms of the chemistry going on. It's geared toward non-scientists as an "easy-to-follow primer."

The Naming of Things

It was clear to me by page 9 that I am absolutely not the audience for this book. The target audience is not expected to have a scientific vocabulary, so many terms are defined and explained in plain English. Generally I applaud such efforts, but the author's expectations for his readers' vocabulary are inconsistent. For example, he defines homogeneous versus heterogeneous mixtures and but doesn't explain what he means by "conjugated" molecules. Anyone who has every purchased homogenized milk could probably take a stab at a working definition of homogeneous, but conjugated? No way.¹ Here's another example (p. 51):

It is viscoelastic like toothpaste, meaning it can liquefy under shear stress and be pumped or extruded easily.

I doubt my non-scientist relatives would be familiar with shear stress and extrusion, even when compared to toothpaste.

The Power of an Editor

I'm not sure if the author had an editor. If he did, that person needed to be more heavy-handed with the red pen. The entire book is a disorganized jumble. There is no flow from chapter to chapter. There doesn't even seem to be much logic to the order of the chapters. Chapter 1 is on measuring and weighing; take a guess what Chapter 2 is.

Heat? No. Acids and bases? No. Nutrition? No. Proteins, fats and sugars? No, no, no.

Chapter is on foams. Heating, meanwhile, is Chapter 11.

I suspect that this book is a reformatted collection of blog posts, but that doesn't excuse the unfocused and meandering writing. (For one thing, The Joy of x was also a collection of blog posts and it was far more coherent than this book.) The disorganization is even reflected in the structure of the chapters themselves, and even individual paragraphs. For example, this is the first paragraph in the Oxidation of Oils and Fats section of Chapter 13 (Oxidation and Reduction, p. 211):

Oils and fats react with oxygen in ways. That are sometimes beneficial and sometimes undesirable. When cooking oils react with oxygen, they can form compounds that taste bad; they're rancid. But when oils react with oxygen and polymerize into rough insoluble films, they're used in paints and coatings for wood products.

Yum! Paint and wood coating! Gosh, I'm glad he included that in a book on food chemistry. It was totally necessary to include that random fact in the main text of the chapter. /sarcasm

Other paragraphs amount to laundry lists of facts. Lists are fine, but when he claims to explain why and how the chemistry works, saying "it works in A, it works in B, it works in C, it works in D“ doesn't answer why or how. When I consider that not a single fact is backed up – no references, no lists of further reading, not even the names of the people who did the research or the institutions where the work was done – I get cranky. Good science writing tells you where you can go to find more of the details. This book doesn't do that.

Bad Science

And now we get to the real kicker: a bunch of the chemistry in this book is just plan wrong. I could overlook a lot of faults if the science were solid, but it's not, and the parts that I know are wrong make me doubt the whole rest of the book. There were several points when I went "That's pretty cool…if it's true." Without references, I can't know if his sources were bad or his understanding is weak. (I suspect both.) And I'll need to do my own search to find out if those cool-if-true statements have any grounding in scientific fact.

Here's one example of bad chemistry (p. 99):

Since carbon dioxide is a gas, there are no bonds holding it together that have to be broken before it can dissolve [into water].

I read that sentence to two chemist friends and thoroughly enjoyed watching their eyes pop out of their faces and their jaws hit the floor.

The Bottom Line

Don't read this book. It's not worth it. If you're looking for a book on the science of food, stick with the classic On Food and Cooking: The Science and Lore of the Kitchen by Harold McGee¹ or read Alton Brown's cookbooks, which are mostly good at explaining the science. This book just does not measure up and threatens instead to undermine facts with misconceptions.

The Silver Lining

You might ask – as my husband did every time I exclaimed "What?!" while reading – why did I bother finishing the book if I found it so awful? Simple: it could be an excellent teaching tool. There are several examples in this book of chemistry misconceptions that my students may have. Not only can I use these as prompts for my own explanations, I am itching to give one or two of these to my students to have them explain what's wrong.

Okay, the 'carbon dioxide is a gas and has no bonds' statement is crap, but why is it crap? How do we know that it's wrong – and what experiments could we do to test it? What misunderstanding of chemistry underlies the statement? How can we change the sentence to get the chemistry right?

By the end of freshman chemistry, my students need to have a thorough enough understanding that hearing such statements makes their eyes bug-out too.

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1: Early in grad school, I heard a physicist give a presentation (to a group of chemists) in which she began explaining conjugation. We (the chemists) told her the explanation wasn't necessary; we were pretty familiar with the term. She said something like "how come you all know this?" But conjugation is a major concept in organic chemistry, which we had all taken and she had not. It was a good reminder to me not to take discipline-specific knowledge for granted.

All of that is to say that if a physics PhD candidate doesn't think of "conjugation" as an everyday term, you can bet that a random science Muggle off the street will have no idea what it means.

2: I admit, I haven't finished On Food and Cooking yet, but as far along as I am, I can assure you the science is more sound than in Culinary Reactions.

Book Review: The Joy of x

The Book

The Joy of x: A Guided Tour of Math, from One to Infinity, by Steven Strogatz

The Premise

Steven Strogatz, a mathematics professor at Cornell, had a math blog (On the Elements of Math) at the New York Times for a while in 2010. This is a collection of those blog posts edited into book form.

Fun with math

I read On the Elements of Math when it was new. The topics were varied and interesting,and the writing was clear. It was equally fun to review things I knew (e.g. explaining the Pythagorean theorem by drawing squares on the triangle's sides) and learn about things I hadn't encountered before (e.g. the Hilbert Hotel problem). I enjoyed it and was sorry to see it come to an end.

It has been a few years since then, and I had forgotten the specifics of the blog when I picked up The Joy of x. (It was kind of interesting just to see which parts I recalled versus what felt like new material.) The topics are still interesting, the stories are still chosen well, and the writing is still clear. I think I enjoyed the first few chapters again as much as I had when I'd read them in blog-post form.

But by the fourth or fifth chapter, my enthusiasm started to lag.

The chapters were starting to sound the same. They had essentially the same structure: identify a potential limitation of math, relate anecdote or pop culture reference, explain the problem in the story, end with a punch line. The chapters are short, so it's easy to run through the pattern several times in one sitting, and it gets repetitive quickly.

I set the book aside and read something else. When I did pick it up again, I read only a chapter at a time and found it much improved. It was like returning to the blog: only one post at a time and a break between one and the next. It's a funny way for me to read a book,¹ but it worked.

The Bottom Line

It's a fun survey of mathematics by someone who obviously loves the subject. No math expertise is necessary to follow along. Read it a bit at a time, like it was originally delivered.

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1: I'm a devourer, a binge-reader. I have been known to read lengthy series in a week or weekend and I read the final Harry Potter book in a single sitting the night I bought it. Reading a book in little bites is not like me.

More on career breaks

I have a few more things to say about how taking a break from science/academia could kill a woman's career.

First, the Executive Director of the Elsevier Foundation wrote a letter to the New York Times about retaining women in STEM (emphasis mine):

The work-life balance challenge faced by working women is particularly difficult for those in STEM professions (science, technology, engineering and math). Taking time off the research track can be a potentially career-ending decision for a woman, as she can lose valuable connections and funding.

Career brakes indeed. This letter prompted me to flip the issue and think about it from another side: what if men took more career breaks? The anecdata I have say that paternity leave (or, parental leave, in more generic terms) is becoming more common. Could we make it an expectation that parents will take breaks?

I have heard of a university (but now can't seem to find the article in which I read about it) that stops the tenure clock for new parents automatically. They have to ask for it not to stop, rather than the other way around. This is to encourage people to use the parental leave they have and make using it less stigmatized. It's a simple enough policy that might actually change academic culture. Parental leave is generally a few months, not multiple years, of course, but if we can change the attitudes about short breaks, I think it's possible to make longer breaks more acceptable, too.

Then there's this post at Chronicle Vitae about the proliferation of "quit lit," the genre of essays about leaving academia. I have read a number of quit lit pieces, but what strikes me about the topic this time around is that academia is a place people leave. Not take a break from, but leave for good. In that sense, it's not just women who might be unwelcome to return after time away, though men aren't likely to be accused of "leaning out" in the process.

I have to wonder how much of this attitude is related to the priesthood of science (and academia in general) and the ridiculous notion that "dedicated" scientists are single-minded in the pursuit of their work to the exclusion of other interests or obligations. I'm not sure and have no data to back it up, but I suspect they are linked.

Lastly, here are a few thoughts about working parents, moms in particular.

From an interview with Indra Nooyi, CEO of PepsiCo.:

I don't think women can have it all. I just don't think so. We pretend we have it all. We pretend we can have it all. My husband and I have been married for 34 years. And we have two daughters. And every day you have to make a decision about whether you are going to be a wife or a mother, in fact many times during the day you have to make those decisions. And you have to co-opt a lot of people to help you. We co-opted our families to help us. We plan our lives meticulously so we can be decent parents. But if you ask our daughters, I'm not sure they will say that I've been a good mom. I'm not sure. And I try all kinds of coping mechanisms.

She says "you have to make a decision about whether you are going to be a wife or a mother," but is her husband also presented with the same decisions about being a husband or a father? Maybe, but maybe not.

I also feel the need to invoke the Finkbeiner test on her interviewer, even though she's not a scientist.¹ Until men are asked in equal proportion about how they balance family with work, we have got to stop interrogating women about it.

Finally, go read this post by dinahere about being the daughter of a working mother.

For the first 12 years of my life I don’t remember my father being there for my birthdays or attending a school play. He was busy saving lives in the OR, earning his share of the money and my mother was there for all of those occasions. So, why didn’t his absence count while hers did? Why were her absences so glaring while her presence so fading?

You know why. Women will never be able to have it all because what we think ‘all’ refers to has been pre-determined by a society that will always be stacked against us.

We can't keep blaming women when they don't measure up to an unachievable standard. The culture has got to change.

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1: I'll just leave this right here, in case you haven't seen it yet.

What's next

I defended my thesis in April, and turned in my dissertation at the end of May, but I haven't left my grad lab yet. Here's what I've been up to, and what's coming up next.

Wrapping up

First I'm wrapping up some things. I've been revising and polishing two papers (one is done and submitted, the other will follow shortly), doing a few experiments for my last project, and getting things ready to hand off to the next person.

Most of my dissertation work was about watching the motions of one protein, TcpP, that is involved in the pathway for producing cholera toxin in Vibrio cholerae. Cholera toxin is the compound (a protein complex) that makes you so very sick if you contract cholera. TcpP (along with another protein, ToxR) activates the transcription¹ of the toxT gene. The ToxT protein activates transcription of the cholera toxin genes.

Aside from its role in cholera toxin production, TcpP is interesting because it (and ToxR, too) is bound to the inner membrane of the bacterium. In order to activate transcription, TcpP and ToxR must bind to the DNA, but somehow they manage to do this without leaving the membrane. Since DNA tends to be compacted into the center of the cell², it's pretty remarkable that two proteins on the membrane can find a specific region of DNA and bind to it. There aren't many proteins that bind DNA while bound to a cellular membrane, but there are a few besides these two.

To learn more about TcpP and how it pulls off this trick, we labeled it with a fluorescent protein and watched it move around the cell. My part of this project is done. Another grad student will watch ToxR move around to learn more about how these two proteins interact. So I'm updating my index of data files, checking that any protocols I've revised are up to date, and commenting the Matlab code I've written that he might use for analysis.

My other dissertation project was a collaboration with my labmate Jess, who has been studying fluorescence enhancement by plasmonic surfaces. I've been learning about plasmon-enhanced fluorescence for years, and it still seems a little bit sci-fi to me: by shining light on metal nanoparticles, you can create an enhanced electric field that makes fluorescent molecules shine brighter and longer.³ Jess has been enhancing fluorescent proteins using nano-structured gold surfaces. A while back we began pairing my fluorescently labeled bacteria with her plasmonic surfaces, to see if we can get enhancement inside live cells. We had some success [$] with our initial experiments, and the project has grown from there. Just because my dissertation is done doesn't mean this project is, though. I've been busy with experiments and trouble-shooting throughout June, and Jess will carry it on after I leave.

Shipping out

My last week as a Biteen lab member will not be spent in lab, but at the Single-Molecule Approaches to Biology Gordon Research Conference in Italy. I like the GRC conference style, and I can't wait to hear all the latest and greatest research in the field. It doesn't hurt that the conference is at a resort in Tuscany, either.

After the conference, it's time for vacation. My husband will meet me in Italy, and we'll tour parts of Italy and Germany and visit some friends of mine from my time as an exchange student. Then it's back to the States so my husband can get back to work and I can enjoy a couple of weeks of unemployment (and prepare for the next job).

Moving on

Mid-August I start my new job. For the next year, I will be a visiting instructor at Lyman Briggs College at Michigan State. (Yes, I'm going to be an adjunct.) I'm excited to move to Briggs: the program is interesting, the faculty I've met have all been delightful people, and this job feels like the right thing for me right now.⁴ Briggs students take science classes that emphasize active learning, and "HPS" courses (history, philosophy and sociology of science) that give them context for science in their lives. As I said to several people while interviewing, Briggs is the kind of place I'd have loved to attend as an undergrad. I'm delighted to teach there. It's gonna be great.

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1: transcription: just like you can talk about transcribing text, i.e. copying words from one place to another, we talk about transcribing genes: copying nucleic acid "words." The nucleic acids are slightly different—DNA is copied into RNA—but both kinds of nucleic acid "words" are the instructions for building proteins.

The process of decoding RNA to protein parts is called "translation." Again, it's just like text, translating from one language (e.g. French, or, in the case of genes, nucleic acids) to another (e.g. English or, for proteins, amino acids). Stitch those translated words together, and you get functional sentences (or proteins!).

2: In eukaryotic cells, such as your own human cells, DNA is stored in the cell nucleus. Bacteria don't have nuclei, but they still keep their DNA kind of bundled up in the middle.

3: It's more complicated than that, but that's the general idea.

4: It's a one-year position, and that suits me fine. My long-term goal is still to get a tenure-track position or a permanent position off the tenure path—I want more certainty in my employment than adjuncting is likely to supply. For the next year, though, I'm very happy to teach at Briggs.

A one-year appointment also means I will go through the whole job application process again this fall. Yay

Career brakes

From SciLogs:

When Adam Spencer asked if female scientists should consider taking an extended break of two or three years, the answer was a resounding “No.” “Science is really a fast-moving world,” [Suzanne] Cory said. “If you get out, even for three years, it becomes very difficult to get back in.

I have heard that position many times from both men and women, and I find it repugnant. It’s a “that’s the way it is” kind of attitude.

My grandmother was a music teacher before she was a mother. She’s told me if she could do it again, she would have become an accountant, but that’s not something girls did in those days. Girls could become teachers, nurses or secretaries. And then they could become mothers. Boys could become accountants or scientists or doctors or lawyers or whatever else they wanted. “That’s the way it is.”

Well that’s not the way it is now, and thank goodness. Thank goodness that somebody stepped up and said “This is what I want to do, and my gender doesn’t matter.” Thank goodness for the women who took the hard path – and the men who helped them – so that I could become a scientist. So that I could be treated as an equal.

Does my expertise have an expiration date? Does leaving the lab for more than a month make me forget how to be a scientist? Will my PhD turn into a pumpkin after midnight? No.

But “science is a fast-moving world” they insist. So what? We all had to learn how to get into that world once, so why can’t someone do it a second time? People also change fields and get into new topics they haven’t studied before. How is that any different from “getting into” the world of science after time away? No, the “fast-moving” argument strikes me as justification to leave things as they are and not bother to make it better.

It galls me to think that women are told that if they leaves, they will not be welcome back—that a career break soon becomes a career brake.

The panel in the article was discussing “possible solutions to fixing this leaky pipeline.” Their conclusion appears to be that women shouldn’t leave in the first place.¹ But why on earth don’t we do something to support the women who want to come back?

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1: Suzanne Cory:

“You are at a crucial age now. Don’t drop off.”

The panelists also said that women need more confidence. Tell me just how much confidence I’ll have after I’ve been told time and again that it’s damn hard to be a woman in science and you can’t leave because then you’ll have let down Womanhood and leaked out of the pipeline, and if you do go you won’t be welcome back because Reasons. And how far will that confidence get me when my words are ignored until spoken by a man? How confident do I need to be to get men to stop patting me on my head? How much confidence will I need to muster to get a seat at the table and be able to keep it?

I have sworn off Women in Science luncheons because I’m sick being told that the solution for the leaky pipeline is “Believe in yourself,” like if I just close my eyes and click my heels together, that will just fix everything.

MATLAB Tip of the Day: Counting in the Command Window

This is actually a two-fer: padding a number with a variable number of leading zeros or spaces and updating text in the Command Window without creating a bunch of new lines.

Variable number padding

The sprintf function includes in its documentation the instructions for padding a number with leading zeros.

myNumber = 4
paddedNumber = sprintf('%02d', myNumber)

paddedNumber =
        04

But what do you do when you don't know how many zeros you'll want to use? You need another variable. The syntax looks like this:

paddedNumber = sprintf('%0*d', numDigits, myNumber)

If I specify numDigits, I can pad myNumber with any number of zeros I choose. Of course, I need to define numDigits somehow. In the FrameCounter function below, I want to have enough leading zeros that my last frame has no zeros out front. So if my last frame is 123, I should get two leading zeros for numbers less than 10, one leading zero for numbers up to 99, and then no leading zeros for the rest. Here's how I like to do it:

numDigits = length(sprintf('d', lastNumber));

This is to say, I write out the number as a string and calculate how many characters that is (i.e. the length of the string). That's how many digits I need to do the padding. Simple.

Updating text in the Command Window

I was using a program in MATLAB that took a long time to run and had an unfortunate tendency to crash¹. I wanted to know which frame it had been working on before it failed, and in general I wanted to have some idea how much progress it had made. At the time, I wasn't aware of the built-in progress bar, and then I learned that that can actually slow down whatever process it is you're trying to keep tabs on, so I wrote my own. It just printed the current frame number to the Command Window every ten frames or so, which was enough to narrow down the range of the failed frame. Every time a new frame was printed to the Command Window, though, it made a new line, and after thousands of successful frames, I had a Command Window full of numbers. What I wanted was a way to update the number in place, without printing a new line.

In 2011, I went to the CPLC Summer School at UIUC (which was pretty fun and enlightening) and I saw what I wanted in action in an analysis program. I didn't have a chance to look at the source, though, so I asked how it worked. The student I was working with said he didn't recall for sure, but he thought it had something to do with backspaces. That clue was enough for me to figure it out on my own.

Here's how it works:

1. Print the text you want to display to the Command Window using fprintf.
2. Print enough backspace characters (again, with fprintf) to delete each of the characters that need to change.
3. Print the new text.

Getting it to work as a separate function took a little thinking, but turned out to be pretty simple. The result is below. I hope you find it (or its components) as useful as I have over the years.

FrameCounter

function FrameCounter(first_num, last_num, current_num, show_text)
%%  Determine the number of digits in the number
num_digits = length(sprintf('%d',last_num));
text = 'Frame ';
if nargin < 4
    show_text = 0;
end
%%  Before displaying the first number
if current_num == first_num
    if show_text == 1
        %%
        % Display "Frame " before the numbers
        fprintf(text)
    end
    for aaa = 1:num_digits
        %% Prime the counter with spaces
        fprintf(' ')
    end
end
%% Remove the previous number
for bbb = 1:num_digits
    fprintf('\b')
end
%%  Display the current number
fprintf('%0*d', num_digits, current_num)
%%  Last number
if current_num == last_num
    if show_text == 1
        char_num = length(sprintf(text));
    else %if show_text == 0
        char_num = 0;
    end
    backspaces = char_num + num_digits;
    pause(.1) % Without this pause, the last number sometimes doesn't display properly.
    %% Remove last number and "Frame " text
    for ccc = 1:backspaces
        fprintf('\b')
    end
end
end

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1: The source of the crash was a read/write conflict with the Windows 7 indexing system. More on that conflict here if you're interested.

The best scientist I know

Joe Palca asked me on Twitter this morning,¹

Who is the best scientist you know, and what qualities make her/him the best?

I had to think a moment about this. I'm sure many people who love science have a favorite historical scientist. My shortlist is mostly crystallographers: Kathleen Lonsdale, Dorothy Crowfoot Hodgkin, the Braggs (Sr. and Jr.), Linus Pauling,² and I am amused by the story of Alessandro Volta, who was such a great practitioner of the scientific method, that he felt the need to zap himself with his electro-motive apparatus over and over again on various parts of the body "where the skin is very delicate" to make sure it really worked.³

Who is the best scientist you know? It's a simple enough question, but it can be interpreted in several ways. For one, what sense of "know" are we considering?

• Who is the best scientist you know of?
• Who is the best scientist you have seen (at a conference, seminar, etc.)?
• Who is the best scientist you have met?
• Who is the best scientist who knows your name in return?
• Who is the best scientist you know personally?

Then we should consider what we mean by "best scientist"? The follow-up question (what qualities…?) allows us to define our own criteria for best, but who gets to be a scientist? Must we consider only professional scientists?

Because this question has so many variations, I have several answers. Here are two scientists I aspire to be more like.

W.E. Moerner is one of the best scientists I know. I have heard him speak on a few occasions, and I have read a fair number of his papers. My advisor was a postdoctoral fellow in his laboratory, and from comments she has made over the course of my PhD, I believe that experience has significantly influenced her approach to science and advising.

Dr. Moerner gave a seminar at UM once, and I was among the students and post-docs who ate lunch with him. We had sandwiches and chips in the Biophysics conference room, and he chatted with each and all of us about a variety of topics. Someone asked him about his work with Kador on single-molecule spectroscopy, and he jumped up to the white board and started sketching out diagrams and explaining the story. He did so clearly and carefully, and seemed to have all the patience in the world when someone didn't understand. He has a reputation for being brilliant, and that made me a bit intimidated at first, but that feeling wore off quickly. He was approachable and just plain excited to tell us about the neat things he'd learned. And he didn't just talk to us, he conversed with us.

Krishanthi Karunatilaka is one of the best scientists I know personally. She was a post-doc in our lab until last fall. She is absolutely meticulous; I have some real notebook-envy for her tidy, organized notes in clear and even handwriting. She is driven and dedicated without any of the pushiness that I have come to associate with those terms. She has worked some long, hard days because she wants to know the answers to the questions she has. She also finds balance. I know that her Saturday mornings in Ann Arbor were set aside for a peaceful cup of coffee on her apartment balcony. She doesn't get knocked down by failures. If an experiment doesn't work (or gives unexpected answers), she has another idea, she keeps rolling on. When someone else is struggling, she's the first person to say "Don't worry, you can try something else. Keep going." She has a talent for presenting even brand-new data in a way that makes it sound like she's considered their implications for weeks.

Other names come to mind as well,⁴ but you'd find they follow the same pattern: the best scientists I know do good, thoughtful, careful scientific work, and are also excellent teachers, communicators, and just generally nice people.

So those are my "best scientists." Who are the best scientists you know? What makes them the best?

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1: I admit, I had a complete fan-girl moment.

2: I admire Marie Curie, too, but she is used so often as The Token Female Scientist, that I think of the words of Mr. Bennet: “That will do extremely well… You have delighted us long enough. Let the other young ladies have time to exhibit.”

3: From Volta's letter to the Royal Society:

If, by means of an ample contact of the hand (well moistened) I establish on one side a good communication with one of the extremities of my electro-motive apparatus … and on the other I apply the forehead, eye-lid, tip of the nose, also well moistened, or any other part of the body where the skin is very delicate: if I apply, I say, with a little pressure, any one of these delicate parts, well moistened, to the point of a metallic wire, communicating properly with the other extremity of the said apparatus, I experience, at the moment that the conducting circle is completed, at the place of the skin touched, and a little beyond it, a blow and a prick, which suddenly passes, and is repeated as many times as the circle is interrupted and restored.

4: For example, my introduction to Jenny Glusker was similar in many respects to my lunch with Dr. Moerner.

Victor DiRita, a collaborator and dissertation committee member of mine, is another one of the best scientists I know. He teaches me something every time time we meet, even if only for a few minutes.

The best amateur scientist I know is probably my uncle Tom, for lots of the same reasons. He is also the only person I know who gets really excited about moss.

Swift

I got an iPod Touch in 2009¹ and wished from the start that I could write my own apps for it.² I knew approximately nothing about coding, though, so it was a rather far-away sort of wish.

In grad school I learned to code in Matlab. It was a sink-or-swim kind of thing. With the help of another grad student, two books, the wonders of Matlab Central (and later StackExchange), and lots of practice, I learned how to write and debug programs.

My brother is a programmer, and by his standards I'm a hobbyist at best, but I can make the computer do what I need, and I've gotten better as I've gone. Still, he teases me about how I should learn a "real" language, and I kind of agree. So about a year ago, after listening to a Mac Power Users episode about learning to code, I bought a book about learning Objective-C.³ I got a little better than halfway through it before other things got in the way; it's one of the things I was planning to come back to this summer between grad school and job.⁴

Those summer plans may have just changed, though. A week or two ago at the WWDC Keynote, Apple announced a new programming language called Swift and I think I'm in love. I watched the demo and thought "I can definitely do this." I may finally be able to write the apps I wished for. There's an eBook about the language, which I've already started reading. Though it starts from "Hello world," I don't think it would be much help if you had no familiarity with programming whatsoever,⁵ but it does look promising for someone (like me) who has at least dipped their toes into the programming pool before.

So that's my next side project: learn another language, try to make an app (I have several ideas), and see how it goes. I'm excited to get started.

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1: Nearly 5 years later, it's a bit sluggish but still kicking.

2: I was also bowled over by the idea that the device playing podcasts in my pocket had a bigger hard drive than my laptop's original drive: 64 vs 60 GB. When I stop to think about it, it still amazes me how powerful the gadgets in my pockets and bags are. And then I start feeling old…

3: It's a really good book, too: The Big Nerd Ranch Guide. My inability to finish it has much more to do with being an overwhelmed graduate student in need of "off" time for my brain than the quality of the book. I highly recommend it, and I think it's an excellent example of instructional writing.

4: Oh yeah, I accepted a job about the same time I was completely overloaded with dissertation and defense stuff. The defense is done, the dissertation is submitted, and though I wrote about the stresses and thrills of job-hunting, I guess never did mention here that I did accept an offer. More on that another time. Short version: I have a job starting in August and I'm excited about it!

5: This is actually the same gripe I have about the Matlab Getting Started Guide and books for "beginners." All of these say that you can start from scratch, but they usually assume knowledge and vocabulary that a first-time programmer may not have. (I'm looking at you, floating-point array.)

Consider these programming languages like human languages: the Getting Started Guide might tell me how a verb is conjugated, but if I don't know what "conjugation" is, I don't know what to do with that information. If you've learned another language before, you've probably learned the meta-terminology already, and have some kind of structure for understanding this new set of words, sounds, and grammar rules.

Many kinds of good scientist

I saw this article by Adam Ruben make the rounds on Twitter a few days ago. Then I saw the article spreading on Facebook, with friends from grad school saying things like "So true!" and "That's totally me!" so I took a look.

He had me until the grants ("I dread writing grants…") but then I realized I wasn't even a third of the way through his list. It just went on and on, with an increasing tone of whininess. The post spirals out into a humble brag. By the time I got to the mice he's killed, I just grumbled, "Okay, dude, we get it. Poor you."

If you can sift through it, though, he makes some points about the culture of academic science that are worth expanding on.

I am not a priestess of Science

• I don’t sit at home reading journals on the weekend.
• I have skipped talks at scientific conferences for social purposes.
• Sometimes I see sunshine on the lawn outside the lab window and realize that I’d rather be outside in the sun.
• I have gone home at 5 p.m.

I love being a scientist, but I have a mighty big problem with the idea that as a scientist (or more broadly, as an academic) I'm supposed to "devote my life" to my work. That's not called Science, that's called Workaholism. If that’s what you enjoy, then by all means do it, but don’t expect me to have the same desires.

Here's my own confession: I worked roughly 8:30-5:30 five days a week through grad school. Sometimes I would keep working when I got home, but that didn't happen every week, much less every day. I came in to work or worked at home a few weekends, but I never made it a routine thing.

It's not that I wasn't dedicated to science or my research project. It's not that I didn't care, or that I was lazy. It's that I needed balance. For the most part, I leave work at work, and I am home at home. Balance for me means lunchtime chatter with friends, Friday date nights with my husband, and brunch with the in-laws. It means taking holidays and coming to work focused. We talk and talk about "work–life balance," but the cultural incentives are heavily on the side of more work and not at all balanced.

The summer after my freshman year, I spent about three months as an REU-type student at Duquesne University. It was awesome, and I learned so very much. An important part of what I learned, though, was that I needed to Stop. I lived in a dorm, worked in the lab, and knew almost no one besides the people I worked with. I ate breakfast in the dorm room, lunch in the lab break room, and dinner back in the dorm room. I had a crappy-to-okay Internet connection, I didn't know my way around Pittsburgh (and was honestly a little frightened of wandering the city alone), and I was too shy to get to know the other girls on my floor, so I stayed in and read research papers. I read a lot of articles that summer. I still have them all, in a cardboard box tucked at the back of a closet. I didn't understand half of what they said on the first read-through, so I read them over and over, looked up terms online, asked questions in the lab, and just tried to work it all out through context. At the end of the summer, I was praised for my efforts, but I was also teetering towards burn-out. I hadn’t spent enough time away from science.

I have been very careful since then to take breaks and disconnect from work. I have sought balance. And I have advised newer students to be mindful of their own balance. I love my science very much, but I refuse to pass on the idea that the only way to succeed in science is as part of a monastic order.

I am not a priestess of Science. I got a PhD all the same.

A PhD is not proof of knowing everything

• I remember about 1% of the organic chemistry I learned in college. Multivariable calculus? Even less.
• I have felt certain that the 22-year-old intern knows more about certain subjects than I do.
• I have pretended to know what I’m talking about.
• I find science difficult.
• I have worked as a teaching assistant for classes in which I did not understand the material.
• I have taught facts and techniques to students that I only myself learned the day before.
• I have feigned familiarity with scientific publications I haven’t read. ¹

A PhD is not proof of knowing anything. It's rewarded for "Persistence to a high Degree" as much as anything. It's not about facts you've memorized, or stuff you can recall on demand–no matter what certain committee members may say. It's about learning something new. And that new stuff wasn't in the classes you took. (As I've discussed with some friends and labmates before: course material covers stuff someone already knows; research is stuff we don't know yet.)

The work you do in a PhD is, as a rule, highly specialized and focused. I spent most of 5 years watching one protein in one pathway in one kind of bacteria. I am the world's expert on the motion of that protein. Yippee. I don't have equal expertise for other bacteria, or even other proteins in the same bacteria, much less other aspects of microbiology, microscopy and the rest. But I do have some expertise, and I have much more in these particular fields than a friend who has studied the thermodynamics of two dimensional structures, or another friend who has studied the surface chemistry of semiconductors. The three of us have each spent 5 years studying chemistry, and we have each earned a PhD for doing so, but we would not be able to pick up each other's projects on a whim. It would take more time and more learning. The need to learn something new doesn't make us bad scientists.

We have got to get over the idea that we must know everything, that everyone around us knows everything and expects the same of us. It's just not true, and it sets unrealistic expectations.

Academics posture too much

• I have asked questions at seminars not because I wanted to know the answers but because I wanted to demonstrate that I was paying attention.
• I have worried more about accolades than about content.

I don't understand why seminars start with the speaker's professional biography. It's not like it'll convince me to come see the talk: I'm already there, sitting in a seat. And if you were to tell me the speaker is from Nowhere State and has done absolutely nothing of note, I'm still not about to get up and leave. Will the talk be better because I now know that Dr. I-Never-Heard-Of worked with Dr. Famous? Fame, publication record and grant money are no guarantees for talk quality, yet those are the things chosen for introductions.²

With fame so highly valued, I suppose it's no surprise that people (in my experience, mostly men) feel the need to show off. Asking a question brings you to the attention of the seminar speaker and the audience. If you don't care about the answer, please don't ask the question; you're just wasting everyone else's time with your ego-stroking. Let someone else ask the question they care about. This counts double for "questions" that don't ask anything. Those are called statements. Keep them to yourself during the open Q&A.

Most scientists don't communicate well

• I can’t read most scientific papers unless I devote my full attention, usually with a browser window open to look up terms on Wikipedia.
• When a visiting scientist gives a colloquium, more often than not I don’t understand what he or she is saying. This even happens sometimes with research I really should be familiar with.
• When I ask scientists to tell me about their research, I nod and tell them it’s interesting even if I don’t understand it at all.
• I have used big science words to sound important to colleagues.

I like words. I like big, fancy words and unusual words and old words hardly anyone uses, but if you study too long for words of four syllables,³ I lose patience. Tell me how you rowed the boat gently down the stream, but not how you 'propelled the craft placidly through the liquid solution.’⁴ I'll know you're smart by the clarity of your point, not the frills in your sentences or the jargon you use. You don't have to emulate Newton and hide your knowledge in nonsense sentences.

Scientists are people

• Sometimes science feels like it’s made of the same politics, pettiness, and ridiculousness that underlie any other job.

Sorry to break it to you, fella, but science is like any other job. There are politics and pettiness, rudeness and ridiculousness. There are easily bruised egos. There are liars and cheats. There are people doing this job, flaws, fears and all. We scientists aren't a special case.

This is what a scientist looks like

As a counter to Ruben's concept of a scientist, here is my own list:

• Science is my job, not my life.
• I do not know everything.
• I do not need to know everything.
• I do not learn by pretending to know.
• My knowledge is not spoiled by sharing it with others.
• I am not perfect.
• I am a scientist anyway.

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1: Another article I read this week was on feigning cultural literacy. It's worth a read. There's a lot of overlap here.

2: Possibly the worst scientific talk I have ever sat through was given by a Nobel laureate; it was absolutely dreadful.

3: “…he does not write with ease. He studies too much for words of four syllables. Do not you, Darcy?” – Mr. Bingley, Pride & Prejudice

4: In case you're not familiar with the “sophisticated version" of "Row Your Boat"

Propel, propel, propel your craft
Placidly down the liquid solution.
Ecstatically, ecstatically, ecstatically, ecstatically,
Existence is but an illusion.

They call me Dr. Haas

Good morning. How are you? I'm Dr. Worm Haas.
I'm interested in things.

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As of today, I've officially completed all the requirements for my PhD.

So I'm not a real worm, but I am a real doctor.¹

Dr. Worm has been stuck in my head for a few days. Now you too can share in my joy/misery.

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1: As my grandmother joked: I'm not a "real" doctor, either because I'm not "the kind that helps people." (She agrees that a PhD is helpful, too.)

Some things I've enjoyed recently

• Type:Rider, a game about the history of typography. It's beautiful and fun.
• This post at Wandering Scientist. I love the two quotes at the end.
• This post at the Chronicle of Higher Education blog. I'm bothered whenever I hear someone preaching about the "real world" and how students aren't prepared for it. The "real" world is full of real people who should be treated with respect and kindness. We gain nothing by dismissing our students.
• Forbidden Island, my new favorite puzzle (it's a digitized board game, but I've been playing the local multiplayer solo)
• 2048, which has usurped sudoku as my go-to time-waster. (Thanks a lot, @chemjobber)
• iThoughts, an iOS/Mac mind-mapping app I've used for a year or two that was recently updated with some nice improvements.
• This post at Penny Arcade on the use and purpose of Twitter was amusing. I also worry at times that my tweets aren't "good enough." Plus, I have a soft spot for Austen references.
• This Periodic Table by Compound Interest is pretty cool.
• It's not nearly as recent as the rest of this list, but I've really been enjoying the Points of Significance column at Nature Methods, and the Points of View column before it. My statistics background is much weaker than I'd like, so it's nice to have a primer. Points of View is similarly helpful for tips on designing figures.

Thanks

I want to take a small break from my thesis-writing to thank some folks for the very kind things they've said about me and done for me lately. First, thanks to you, reader, for stopping by my little corner of the big wide Internet. And thanks to those of you who have enjoyed it enough to pass it on elsewhere. It's pretty exciting (and honestly a teensy bit scary) to see your words quoted and linked on somebody else's blog, recommended on Twitter, and highlighted as a thing worth reading. There are only so many hours in a day, and I am delighted that there are people who find my words worthwhile enough to spend some of that precious time on.

Attention

More thoughts from my trip to San Francisco. This really happened, and though you may think it's "not so bad," it still shook me.

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We waited for the light to change. A fire truck rolled past, and one of the firefighters caught my eye and waved to me. I smiled. It seemed friendly. Yes, potentially flirtatious, but certainly benign.

I left the group as they entered the dance club. Tired feet took me downhill to the hotel. Four men hiked the hill in the other direction. As they approached, one called "Hey." It wasn't a greeting; it was an invitation to a conversation. I pretended not to hear and kept walking.

Another intersection. Another crosswalk. Another light slow to change. A man carrying a shopping bag neared the same stop. He skipped right to "What are you doing out tonight? You're a sweet little thing. You want to get something to eat?"

My training in politeness kicked in, even though he stepped closer, approaching my shoulder, step by step. "No thank you. Have a good night," I said, glad the light had finally turned.

I realized then that those four men walking uphill had triggered something in me. I had weighed them as a possible threat and found them unlikely to be trouble. It was unconsciously done. But the lone man on the corner tripped my alarms and reminded me that those alarms even exist, that out on the street I am always judging men–and occasionally women– for their potential to cause me harm. And that fact scared me.

Someone looking at me would see I was wearing a black pea coat, jeans, and sneakers. Not exactly dressed for attention. It was 1 am. But it doesn't matter what I was wearing, and it doesn't matter what time of day it was. I shouldn't have to spend my energy shielding myself from unwanted attention.