30 Days

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It's NaNoWriMo time again. I'm not planning to write a novel, but I do think I ought to write more often. So here is my challenge: I will write something worth posting every day. It might be very short, and it might not be posted the day it is written (typos show up easiest when they're most likely to be embarrassing, after all), but I will write something every day in November. And maybe by then I'll have made writing a more frequent habit.

This is not today's post. That felt like cheating. I have something else written that will go up later.

Doctor? When?

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Reading Paul Bracher's recent post on titles, I was a bit bothered that all of his examples were of men. Admittedly, he is male, and so, if he's speaking about his own perspective, male pronouns make sense, but this didn't have to be male only:

You'll find that I'm pretty liberal in using "Dr." when addressing letters and e-mails, because you never known when someone is going to get upset at being called "Mister."

When are you nearly guaranteed to upset someone by calling them "Mister"? When that someone is female.

One of my college professors–let's call her Dr. Smith–kept her maiden name after marriage, like plenty of other academic women do. She and her husband –let's call him Dr. Jones–were introduced at an event as "Dr. and Mrs. Jones." In that moment, she lost her name and her title to the old-fashioned assumptions that Dr. = Mr. + PhD, and that a married woman always takes her husband's name.

Another commenter at ChemBark described one of my own fears along these lines:

…sometimes those students would call a male professor "Dr." but then use the title "Ms" or "Mrs" with me (While we were in the same room! And with a male professor who was my age!)"

So Paul Bracher can go by Paul if he wants, but when I am an instructor, can I go by Beth? This time next year, I will be Dr. Haas. If I don't insist on the title, will I forfeit the respect that comes with it?

When to speak and what to say

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Several events have gotten tangled in my thoughts over the last week, and they've made me consider when and how to say you've been hurt.

Last week, a group I participate in came to a decision in a way that hurt and disappointed me. (The exact details aren't important here, and I don't want to open old wounds.) I emailed the group about it and asked that we find ways to do better in the future. A leader of the group 'thanked me for my honesty' and told me that my message was not an appropriate use for the group email list. That particular leader did not otherwise acknowledge my concerns beyond excusing that person's own part in it. When the group met next in person, the same leader "reminded" the group about proper use of the group list.

Over the weekend, the corner of Twitter I stick my nose into blew up when Dr. Danielle Lee wrote about a very rude encounter she had, and her blog network pulled the post. Plenty of digital ink has been spilled on the subject already, so I refer you to elsewhere for the recap.

As the dust settled on that case, Monica Byrne came forward with the name of the man who sexually harassed her a year ago. It didn't take long for people to tell her she should not have done that.

My own hurts and disappointments are on a much, much smaller scale than what Dr. Lee and Ms. Byrne have so recently experienced, but they share some similarities: we've all spoken up about a way we felt wronged, and someone has felt the need to tell us that it wasn't the right time, place, or way to say what's on our minds.

If not now, then when? If not in public, then where am I being sent to hide? If not this way, then how shall I tell you? Heaven forbid the pain of one person should inconvenience another.

My hurts are small. I will heal quickly. But I wonder, when do you say "I have been hurt,"? How do you start the conversation? Must I always expect my audience to include an advocate for silence?

MATLAB tip of the day: Toggling scales

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The Problem

Some of the figures I create can be presented on either logarithmic or linear scales. After creating a plot, I may want to switch scales, but I don't want to type set(gca, 'XScale', 'log') every time (nor do I want to pull it out of the Command History). I want a faster way to switch between lin and log axes.

My Solution

A shortcut, of course. I love shortcuts. This shortcut determines the current scale used for the selected axis, and switches the scaling to the other choice.

Here's the code:

% Toggle scale of Y axis
scaleType = get(gca, 'YScale');
switch scaleType
    case 'linear'
        set(gca, 'YScale', 'log')
        disp('y scale is now log')
    case 'log'
        set(gca, 'YScale', 'lin')
        disp('y scale is now linear')
end

I have two such shortcuts, one for X, and one for Y. (Obviously, for X, you swap in 'XScale' for 'YScale'.)

On Impostors

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I've been catching up on my podcast backlog, including Back to Work Episode 132, wherein Dan and Merlin discuss frauds and impostors. Dan had never heard of Impostor Syndrome, and has no sympathy (but plenty of suspicion!) for anyone who says they feel like a fraud. Merlin said he's felt like a fraud, but then the two of them go around and around saying variations of "That's so silly, why would you feel like that? Stop feeling like that."

Thanks, guys. So helpful.

Let me tell you a bit about feeling like an impostor.

I regularly feel under-qualified. Like I must have -- unknowingly -- tricked people around me into thinking that I know what I'm doing. In my eyes, I'm just a country kid with some fancy papers on the wall. The people I'm surrounded by are so smart, and work so hard, and know so many things. And sometimes I feel like a hayseed.

I have to reassure myself that I belong here. It's not something I know, it's something I must actively remember.

My very first day, I met students from Berkeley and Cornell et al., who referred to textbooks by the authors' names and mentioned famous faculty like I might mention the weather. As far as I knew, my textbook was called "Chemistry." My alma mater is practically unknown outside its region, and it has such a confusing name that I know exactly each step in the getting-to-meet-you dance.1 So there I was, surrounded by students from "better" schools. It was absolutely intimidating.

Now, four and a half years later, I counter that comparison with another: I'm still here, and plenty of students with more prestigious pedigrees couldn't hack it.

Knowing that I'm not a fraud does not stop me from feeling like a fraud, though. It creeps into Q&A's (What if my question is stupid?), it follows me to conferences (I didn't understand that speaker at all; better not say anything), and it nags me as I work through my project (What if I'm wrong? What if I overlooked something? I know so little about this calculation or protocol or field…).

You know what doesn't help this feeling? Hearing that someone else suspects that frauds are everywhere. (Ahem, Dan: "I think the opposite [of Impostor Syndrome] is more common.")

You know what else doesn't help? Being told that your feelings are silly and so you should just change them. It's like telling someone with depression to cheer up, or telling someone with anxiety to stop worrying.

So what does help?

I keep a "Feel-Good File" of positive feedback, and I read it when I begin to doubt. I remind myself of the reasons why I do belong here. I remind myself that I am likely not the only person in the room worried of being found out for having flaws. I forgive others for making mistakes.

It's hard to be successful if you aren't willing to take risks, and it's hard to take risks if you're afraid of being wrong. If you feel like an impostor, you're very afraid of being wrong.

If I do this thing, people may judge me for it. They will find out that I don't actually belong here. They will know I have deceived them. They will not trust me.

The other thing that helps? Knowing that you're not alone.

1: You're from where? That's a funny name. Is that part of (totally unrelated famous university)?

MATLAB tip of the day: Toggling figure visibility

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The Problem

Usually I like to see MATLAB figures as they are produced, but if I'm running a long script, visible figures can clutter the screen and hog the available memory. I wanted a way to change visibility quickly, easily, and without having to remember how I did it.

My Solution

I wrote a small script that toggles the DefaultFigureVisible state, and popped that into my Shortcuts bar. Now I can just click the shortcut whenever I want to change the state.

Here's the code: 

% Toggle figure visibility
state = get(0, 'DefaultFigureVisible');
switch state
    case 'on'
        set(0, 'DefaultFigureVisible', 'off')
        disp('Figures are off.')
    case 'off'
        set(0, 'DefaultFigureVisible', 'on')
        disp('Figures are on.')
    otherwise %In case something goes completely nuts 
        disp('No change made.')
        disp(state)
end

MATLAB tip of the day: Invisible figures

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Problem

MATLAB *.fig files won't open.

Key Symptoms

  • when double-clicking on a *.fig file in a folder, no figure is shown in MATLAB; e.g. on a Mac, after double-clicking the file, you see the opening animation, but no signs in MATLAB that the file actually opened
  • no error message is displayed in the MATLAB Command Window
  • after an unsuccessful attempt to open a figure file, entering figure into the Command Window produces a new figure window labeled Figure 2 (or greater), not Figure 1
  • figures made previously open normally
  • affected figures do not open on other instances of MATLAB

Cause

About the time your figures stopped showing up, you probably turned off figure visibility. Setting figures invisible by default sets the figures invisible, including the files saved. That is, it's not a switch for the display of figures, it's a switch for the figures themselves.

Solution

There are several ways to make those figures visible again, but my favorite solution (to a problem that I don't think should exist in the first place) is to make a copy of the openfig function, and change the line for the default behavior (which is set to respect the visibility status of the figure file) to visible. Save that customized openfig function to your MATLAB directory, and you're all set.

Before I found this answer, I was despairing that I'd have to remake dozens of *.fig files that wouldn't open. When I saw this page, I realized that I had encountered (and corrected) this problem once before. To save myself – and whoever else comes across this post – some heartache, I decided to write it up.

IOT: Crystallography

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Back in November In Our Time did an episode on crystallography. I just listened to it this week, and it is lovely. I haven't done any work in that field since I started grad school, but I still love it. Despite the huge impact crystallography has had on other sciences, it's a field most people haven't heard of, so it was pretty nice to have it highlighted on the show.

I'm proud to have been part of that excellent community they mentioned, too. The biggest conference I've attended was the IUCr Congress in Osaka, Japan. It was fantastic, and not just because I got to go to Japan. Well organized, great science, good atmosphere and a fairly welcoming attitude among participants. I've been to smaller conferences that were much less inviting.

On the Readability of Old Papers

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Archaic terminology aside, old (pre-1950) scientific texts are surprisingly readable. Perhaps this is partly due to translation, since many early works come to English by way of Latin, French and German, but I suspect that it has just as much to do with the broad audience of the writings.

An early scientist was not a chemist or a physicist or a geologist or a biologist, but a chemist and a physicist and a geologist and a biologist (at least a little bit). In the modern era, scientists have hunkered down into very specific niches. We don't expect someone to be a chemist and a biologist; we praise them for their interdisciplinary-ness and call them biochemists (or chemical biologists, if you'd rather). We forget how to communicate to those outside our niches. I think this has a lot to do with the masses of impenetrable prose published each week, month and year.

I think there are a few other major factors, too; namely the increased pressure to publish more things more often, which could detract from the quality of individual papers; the increased diversity of backgrounds in science, which likely includes a greater population of people who did not study rhetoric than in Dalton's time; and the affectation of intelligence by using fancy vocabulary as a proxy for actual understanding.

Footnotes in Chemistry

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"…the British chemist John Dalton (1766-1844) provided the basic theory: all matter–whether element, compound or mixture–is composed of small particles called atoms."

– Ebbing and Gammon. General Chemistry, 8th ed. (New York: Houghton Mifflin, 2008), 42.

If the quoted text above were on Wikipedia, rather than in a traditionally published textbook, it would be tagged citation needed. Instead it has no reference at all: nothing inline, no footnotes, no endnotes. Nothing. And from a brief survey of chemistry textbooks (the handful sitting on my shelves), this is common.

Articles on super-resolution microscopy often start by describing the diffraction limit. It would be unthinkable not to cite Ernst Abbe's work on the subject. If I were writing for a textbook, though, it appears I could say:

"Ernst Abbe (1840-1905) discovered that the resolution of a microscope is wavelength-dependent"

and leave it at that.

It seems so unscientific to me to provide such conclusions without their accompanying evidence. The exciting questions in science, I believe, come out of why, how and how do you know? and I think a textbook should answer those questions, even if it's just a reference to details elsewhere.

So that's what I'm going to do: find the missing references to the details of major discoveries covered in general chemistry textbooks like Ebbing & Gammon.

Others, particularly Dr. Carmen Giunta at Le Moyne College and the folks behind ChemTeam, have collected some of the classic works online. Dr. William Jensen, of the University of Cincinnati, had a delightful "Ask the historian" column in the Journal of Chemical Education, as well. My hope is that my list will be more searchable and (eventually) comprehensive.

Citation needed

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Why don't chemistry textbooks cite their sources? High schoolers are taught to use references for specific details, but my college-level textbooks state many such details without an ounce of support. How do we entrust our students' learning to books that make unsupported claims?! It's unscientific. How can I be sure that one textbook is not simply misstating another, or propagating another's errors?

Let there (still) be stoning!

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Key points for presenters from Lehr's "Let there be stoning!" Ground Water (1985). Emphasis mine. [1]

The problem

  • "Let there be an end to incredibly boring speakers! They are not sophisticated, erudite scientists speaking above our intellectual capability; they are arrogant, thoughtless individuals who insult our very presence by their lack of concern for our desire to benefit from a meeting which we chose to attend."
  • "Failure to spend [your audience's time] wisely and well, failure to educate, entertain, elucidate, enlighten, and most important of all, failure to maintain attention and interest should be punishable by stoning. There is no excuse for such tedium, so why not exact the ultimate penalty?"

His advice

  • "Never subject your audience to poor slides just because they serve as an outline for your talk."
  • "If you need a pointer to indicate an important concept or location on a slide, it is probably too crowded or difficult to comprehend."
  • "If you can't read the print on a slide clearly with the naked eye (reading glasses are permitted) when holding it in your hand, it is inadequate for viewing with a slide projector in any size room with an adequately sized screen."
  • "Never, but never…show a slide and then apologize for it. Don't show it."
  • "Don't be afraid to use no slides."
  • "If you want to use slides, make them good ones."
  • "Don't stay on one slide too long; put blanks between slides if you have a lot to say before the next slide. The old slide is distracting."
  • "When you are giving a paper, you are an actor on a stage…You're an entertainer, an educator; put on a happy face and kick ass—or get off that stage."
  • "Think of the time the audience is collectively giving you. One hundred people times 20 minutes is 33 hours. Don't you owe them a few hours of effort in return?"
  • "Don't get up and do what comes naturally if what comes naturally is a dull, witless, monotonous presentation of unexciting facts. If your work is in fact dull and unexciting, don't burden any audience anywhere with a conference presentation."
  • "I studied astronomy under a dullard and thought it was a dead science. Carl Sagan taught me differently. … Make your subject—no matter how esoteric—live for your audience if only for 20 minutes."

[1]: via Presentation Zen

Response to "Ten Simple Rules to Combine Teaching and Research"

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Vicens & Bourne, PLoS Comp Biol 2009

My summary of their 10 rules:

  1. Learn to manage your time
  2. Set specific goals
  3. Don't try to do everything
  4. See #3
  5. See #3
  6. See #3
  7. See #3
  8. See #1
  9. Start early, practice often
  10. See #1

Methinks they liked the roundness of 10 in "10 Simple Rules" too much. My approach?

  1. Learn GTD
    • bonus points for learning Inbox Zero, also
  2. Start early, practice often

On Not Knowing and Being Wrong

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Rarely do we have all the facts. We work based on the evidence available at the time, and even then some things may be overlooked.

Consider Alice and Bob. Alice asks Bob for assistance. Bob snaps at her to do her own work and quit bothering him. If Alice does not know Bob well, she might conclude that he's a jerk. If Alice knows that Bob has gotten very little sleep for the last few days and that he has a major deadline approaching, she might conclude that he's stressed out. Without changing the facts, just changing their availability to Alice, it is clear that her conclusion may change.

This is how scientific discovery works. The available facts change all the time, and so our conclusions change. New methods of measurement, new datasets, knowledge crossing disciplines, any of these things can potentially change the conclusions we draw. Often the differences are subtle. Still, if you are in the mindset that conclusions are fixed Truths, finding that you're wrong (again and again and again) can be disconcerting.

At the same time, we can't wait for all the facts before making any conclusions. You may never get all the facts. You'll be stuck in inaction, indecisive as Hamlet.

This is what I struggle with now. Do I have enough facts for a reasonably firm conclusion? Which facts can I collect – which experiments can I run – in the near future that would help? As fun as it may sound, I can't explore forever. It's not a realistic prospect. I need to gather the information available to me now and conclude what I can. Tomorrow's new facts may tell me I am wrong, but I won't know until then.

Surviving Chemistry Seminars

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Considering Chad Orzel's Notes Toward a User's Guide to Synthetic Chemistry Talks, I made a list of questions you can (almost) always ask at a chemistry seminar (not just synthetic):

  • What is the impact of pH on ‹thing you're studying›?
  • What is the impact of temperature on ‹thing you're studying›?
  • What is the impact of solvent[1] on ‹thing you're studying›?
  • What is the effect of concentration/crowding on ‹thing you're studying›?

Riskier – Orzel might say "unsporting" – but often applicable questions include:

  • What impact does ‹thing you're studying› have on the environment/society?
  • What are the ethical implications of ‹thing you're studying›?

[1]: in biological chemistry, substitute "media" for "solvent"

Things they don't tell you about graduate school

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My advice for those just beginning

  • Many, many things may be the way they are because of department/campus/regional politics. (And that's not always bad.)
  • Your advisor is probably making it up as he/she goes along, just like you are.
  • Your students (particularly freshmen) think you are supposed to have all the answers. If grades are involved, they are not likely to be pleased or reassured to find out you are human.
  • Everything takes longer than you think.
  • There is no right way. There are better ways and more famous ways, and those may be two different things.
  • Big name researchers may (and often do) give dreadful seminars.
  • Just because the food is free does not mean it's any good or that you have to eat it.
  • Beware of a group or advisor of whom the highest praise is lukewarm.
  • A group referred to as "dedicated" should be considered with caution. "Dedicated" often means "life-stealing."
  • Hours spent in the lab or office simply to satisfy an attendance quota are not likely to help. Butts in seats ≠ minds at work.
  • Even so, sometimes you just need to throw more hours at a problem.
  • Make friends outside your group. Even better, make friends outside your department. Best of all, have at least one friend you talk to regularly who isn't in grad school at all.
  • Find time to do something that isn't work. Every week. Do not schedule anything else during that time.
  • You will be wrong a lot. Maybe even most of the time.
  • Your conclusions may change every few days or weeks. This is normal.
  • Surround yourself with people who are experts at other things. Ask them for help early and often.
  • Ask for help even if you're not sure what particular help you need. Sometimes the greatest help comes in formulating the questions you need to ask.
  • Don't put up with bullies.
  • Find an advocate. When you run in to trouble, you'll need someone to back you up.
  • That guy who is arrogant and belittling? He's probably afraid you'll think he's a fraud. You don't have to fear him.
  • You are not the only impostor in the room. Everyone else is hoping you won't notice.
  • "I don't know" is a legitimate answer. When answering questions about your research, "I don't know yet" is probably better. You might never know. That's okay, too.

Scientific thought and the endurance of facts

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  • In the pop sci world, facts are frequently treated as solid, immovable things. When commonly known theories change, lay people can get up in arms over the changing of 'facts.'
  • We teach students facts as if they were eternal, but few ideas are unchanging.
  • Every scientific theory was once a hypothesis. Someone had to gather the evidence, take the measurements, and pull together a working idea.
  • Scientific facts are not self-evident.

I think facts are more like stones in a wall. You can build a serviceable, sturdy wall out of rough hewn stones. There may be weak points and gaps. When someone does the hard (and often tedious) work of refining those stones, gaps are closed, and the structure becomes sturdier. Sometimes, despite years of acceptance, we find a stone doesn't fit with its neighbors any more. Sometimes that stone is changed and adapted. Sometimes it is removed altogether and replaced with one that fits better – a theory that explains better.

A key ingredient to scientific thought is falsifiability. You accept – perhaps expect! – that someone else with more evidence could come along and prove you wrong.