IOT: Crystallography

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.

GTD and Learning Objectives

It occurred to me that these are really quite similar, parallel constructions, with the major difference that GTD focuses on what you will do, while learning objectives are about what your students will do. In both cases, you consider first what you want to achieve, and then you carefully think through what specific, concrete, actionable tasks you need to set to get there.

On the Readability of Old Papers

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

"…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

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?

Miscellaneous thoughts on science and science education

I think the scientific disciplines are not so much territories in the landscape of science as viewpoints from which one can look out over that landscape. The boundaries we erect between physics and chemistry, chemistry and biology, and so on, are less like fences separating fields and more like well-worn paths from one place to another.

Let there (still) be stoning!

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"

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

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

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

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

• 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.

Please excuse my brevity

Why do people (myself often included) feel the need to make excuses or ask forgiveness for our e-mails? If I take a day or two to reply[1], or if my message is short, what is there to forgive? Would an immediate, hair-trigger response really be preferable? Would twice as many words really do a better job of conveying my message?

I think the answer is No.

No, a faster response is not necessarily better. No, a longer response is not necessarily better. No, I don't need to apologize for taking time to consider my words, for saying my piece in something shorter than a lengthy epistle, for doing the work I have that is not reading and replying to e-mail. And I certainly don't need to append such an apology to every message I send.

[1]: to a non-urgent matter

On Failure

The definition of insanity [1] is doing the same thing over and over again and expecting a different result.

I hate that saying. I much prefer:

If at first you don't succeed, try, try again.

Why? Because things rarely work the first time, and because “the same thing” is almost never exactly the same thing.

In research we try to account for all the variables, and to hold as much constant as possible. But we can't control everything, and we don't even necessarily recognize all the variables: different time of day, different batch of materials, different weather, different container, different attitude, different anything. And any one of those different things may cause the experiment to fail.

And it may fail again, and again, and again before all the right conditions are met.

Experimental scientists [2] fail a lot. We fail all the time, even most of the time. We learn from our failures, dust ourselves off, and “try, try again.”

Think about that saying:

If at first you don't succeed, try, try again.

It's not “if at first you don't succeed, give up,” or “if at first you don't succeed, you're stupid,” or even “if at first you don't succeed, try again.”

Try, try again. And then try again after that. Once isn't going to be enough.

Don't trust the scientist who has never failed; they're probably lying. Failure is a part of research; it's the challenges and obstacles you puzzle over, work around and overcome. It's the majority of the problems in “problem-solving.”

But it can be demoralizing to fail.

It's pretty easy to conflate “the experiment failed” with “I failed,” and “I failed” becomes “I am a failure” all too quickly, as the tally of failed experiments grows.

Here is the gateway to self-doubt, hanging wide open. Don't walk through; it'll snap closed behind you, and it's hard to climb out.

Laboratory courses, even those founded on “discovery-based” learning, do not teach students to fail. Failure of an experiment is a failure of the student. If classroom demonstrations always have known outcomes and go smoothly, if teaching labs punish failed experiments, aren't the students trained to fear being wrong and trying things that might not work? Of course, it's helpful to illustrate a concept or demonstrate a trend with a successful experiment, but what is the price of this success? A student who fears failure and then begins a research project is unprepared for the “try, try again” part.

Doing something over and over and looking for a different result is not the definition of insanity, it's the definition of experiment.[3]

[1] Sometimes “stupidity” is used instead of “insanity.”
[2] I make no claims about the rest.
[3] experimental : based on untested ideas or techniques and not yet established or finalized

Gender bias and names

I just read "Science faculty's subtle gender biases favor male students," from a recent edition of PNAS. They make a decent case for their conclusion that science faculty are biased against women (despite the title, the conclusion is not pro male, but anti female).

They sent a supposed application to ~160 faculty (at 6 institutions). Half of the faculty were men, half women. Half of the purported applicants had "female" names, half had "male" names. The faculty (both male and female) perceived he female applicant more likeable, but less competent and less hireable. They offered her a significantly smaller salary, and less mentoring. Sounds pretty bleak and biased.

I see a flaw, however. Before I'd gotten even halfway through, I was asking myself "Which names did they choose?" What about gender-neutral names, like Lee? What about perceived nationality or regional differences? What if they called the girl Jennifer?

I like names, and it amuses me to play around with the NameVoyager site, watching the rise and fall of trendy names. I have three Aunts named Barbara, and my husband has another. I have met one woman named Barbara who was born after 1975, and that was while I was living in Germany. My mother has an "old lady name." She has met few women who share her name, and all them have been at least 20 years her senior. And then there are the names that trickle down from the pretentious to the great unwashed. "Freakanomics" (or was it its "Super" successor?) has a great chapter on baby names, perceptions, and the economic status of the name-givers. NameVoyager has a list of poll questions for each name, to gauge (and then report on) perceptions of names. Do they sound smart? Do they sound attractive? Is the name associated with someone famous? Famously unsavory? Based on the kinds of responses there, I doubt there are many Americans naming their daughters Bertha today.

So I thought about all of these name-y things as I read the paper. What names did they choose? The authors insist that the only differed between the applications was the gender of the name, but what about the perception of that name?

Well, they chose John and Jennifer. Yes, Jennifer. I feared as much. The authors say they chose names of similar likeability. I don't think they are names of similar seriousness. Now I know a fair number of Johns and Jennifers, and I certainly won't say they have been the same in abilities, personalities or looks. Still, if you were to ask me for adjectives describing a John, I'd say ordinary, reliable, solid. For Jennifer, I'd say bubbly, cheerful, friendly.

Do those descriptions look gender biased? Certainly. I'd say they match up pretty well with the "subtle bias" the authors are talking about. But does that mean that I would prefer a man over a woman? No. It means I might prefer a John over a Jennifer.

What names might I find more even? How about Jacob and Bridget? Paul and Ann? I'm keeping along the traditional English line that the authors' picks conform to. Why not Mohammed and Saria? Jose and Magda? Horace and Gertrude? Deshawn and Dominique?

They used just one name per gender and then said the perceptions of those two names could represent the perceptions of their respective halves of the population. I find that suspect.

Don't get me wrong: they're still probably right, and it's probably not a good sign that John and Jennifer create such different expectations.

"I'm not a feminist, but..."

A friend of mine started her sentence this way as we discussed the Akin "legitimate rape" debacle. I wanted to laugh and ask her just what she thought a feminist was. I didn't, we kept talking, and she sounded about as feminist as I am, which is to say, Votes-for-Women! feminist, but not Who-needs-men? feminist.

Feminism has a skewed reputation. Until a year or two ago, even I thought "feminist" inherently referred to combat boots and a ban on skirts. I happen to like skirts (and wish I could find a lab-suitable skirt as practical as my blue jeans), and I happen to like being a Mrs. John Smith. Still, I now call myself a feminist.

There's a catch to that. I don't announce that I'm a feminist. Most folks just don't understand, and they'd peg me as a stereotype, or insist that I don't fit said stereotype, so I couldn't possibly be what I say I am.

All the same, I'm a feminist.

As I said before, I'm a Votes-for-Women! feminist. An "anything boys can do, girls can do too" feminist. I believe in equality, not supremacy. I believe in individuals. Let (strong) women be firefighters, and do not pass them over for weaker men. Let men raise their children without the surprise or scorn of their neighbors. Judge each person by the content of their character, not what hides between their legs.

I am a feminist because I believe in women, and I believe they, as a group, haven't yet gotten their due.

---

Perhaps a better term would be "equalist." I believe in equitable treatment for all. Our strengths, weaknesses and experiences differ, but when a stranger meets me, I should be treated the same as the next person, without prejudice. I should not have to fight against false expectations based on my appearance.

On Printers

A watched pot never boils, and in a staring contest with a finicky printer, the printer is near guaranteed to win.

Printers and Ink

Our Epson printer (a two-year old Epson Stylus NX420) is a printer-scanner combo. It's been a very useful flatbed scanner, but its track record as a printer is mediocre. It's quite the thirsty little beast, drinking up ink and howling for more.

This afternoon I tried to print a half-page form allowing UPS to deliver a package while I'm at work on Monday. The printer was out of cyan ink. It didn't care that the page was in black. It was out of cyan ink. And it told me so over and over again. It was out of cyan ink.

To the Internet! I searched for a way to convince my stubborn electronic companion that it was okay to print in black alone, and Epson's own support pages had an answer (which I happened to find in the printer settings on my own about the same time). There is a driver option to allow the printer --temporarily (and this was emphasized)-- to print in black only. Just check a hidden box, set the page to print in grayscale and simplify every other possible setting. I followed the instructions, but the printer would have none of it.

Perhaps there's a way to change those settings on the device itself? Maybe it just needs hardware and software to agree at both ends? No. Once the printer is convinced it is out of any color ink, that sole idea consumes its digital mind. I pressed settings. It was out of cyan ink. I pressed clear. Can't do that. It was out of cyan ink. Even if I lifted the lid, as if I were about to replace said ink, it persisted in proclaiming it was out of cyan ink. After a few go-arounds with this, it would grudgingly slide the cartridges over for inspection and replacement, but there was no fooling it. I could try all the old tricks that once worked: take out the cartridge and put it back it, take out the cartridge and shake it in the hopes the ink would pool near the nozzle, turn it off and on again, try to manually feed a sheet of paper in. Nothing worked. It was out of cyan ink.

Reading reviews online (in the hopes that someone had stumbled across a solution and posted it in a grumpy review), I saw the Amazon page for this printer. The ratings were overwhelmingly ⅕ stars, and most of them had titles that started with things like "beware" or "scam." That's not very consoling. Some pointed out (and I verified this myself) that you can't even scan a document from the device when any of the ink is out. (Yes, you can still scan from the computer, but not by pressing the "Scan" button on the device's panel. It will tell you, as before, that it is out of cyan ink. Of course.)

This is like having a car that won't let you turn on the stereo if it's out of gas. Or perhaps it's like a car that won't start unless its stereo can pick up a radio station. Foolishness. One activity does not depend on the ability to do another.

So I'm done with this printer and its $15 vials of ink. My old printer (a Canon Pixma iP4200, four years older than the Epson) likely hasn't been used more than twice since we bought the printer-scanner. I wasn't sure it had any ink, either, but it printed the page on the first try.

Canon won me all over again, and Epson can bite me.

Redesigning the US Postal Service Website

Every time I want to mail a small package, I check the USPS website for the cost, in the hopes that I can use stamps already on hand, and not have to spend my lunch break standing in line at the post office. I purchase Forever Stamps fairly regularly, but it seems the cost of a stamp goes up every 3-6 months, so not only do I need to find the cost of shipping my little package, I also need to look up the current value of my stamps.

These two simple things -- things that the fellow at the post office counter can usually tell me off the top of his head -- are surprisingly hard to find the USPS website.

When you go to usps.com (Isn't it a government organization? Why isn't it usps.gov?) there is a list of "Quick Tools" on the left, including a link to the postage calculator. In order to find out the cost of a regular stamp (you know, the price you'd expect to hear if you asked "How much are postage stamps?"), you must enter two ZIP codes, pick "Letter" from the Shape selection, and enter a weight. Well how much does a typical letter weigh? I'm not sure, but if you say 1 ounce, you're then prompted with four envelope choices. If you choose the basic, regular old letter envelope, you get a list of 23 delivery options spread across four categories. The first item on the list is Express Mail, and today that option is listed with a "Post Office Price" of $21.30. Down at the bottom of the list is what I was actually looking for: the cost of a basic letter (dubbed "First-Class Mail Letter") at $0.45.

It took three pages, entering unnecessary information (ZIP codes, weights, shape), and looking at the bottom of the list to find out that a regular stamp today is worth $0.45.

The good news is that it's hardly any more complicated to calculate the cost of shipping an oddly shaped package to Timbuktu overnight than it is to get the cost of a basic letter, but I think my point still stands: it should be simpler to find the cost of a stamp.

Now, there is an alternate way to find the cost of a stamp. Instead of going through the postage calculator, you could choose "Buy Stamps" from a dropdown menu. Thankfully someone thought to update the menu on that site so that the Forever Stamps choice is now phrased "Forever/45-Cent Stamps," cluing the observant visitor in to the current cost of a Forever Stamp. All the same, I think that information should be front and center on the postage calculator site. For that matter, I think it ought to be on usps.com.

In my mind, the postage calculator ought to tell me not only how much it costs to ship something, but how many stamps (of the standard values) it would take to cover that cost.

Response to 'Awards for Women'

Awards for Women

Psh.

That was my response. Something between a derisive snort and a laugh.

Highlighting mine:

Programme aims to boost scientific participation for women from 81 developing nations. Five early-career female researchers from Africa, the Middle East, Asia, Latin America and the Caribbean are to be honoured with US$5,000 Elsevier Foundation Awards in a programme to encourage women to pursue science in nations that lack scientific expertise, resources and gender equality. “They are not given the opportunity to do good science,” says Peter McGrath, a programme officer for co-sponsor TWAS, the academy of sciences for the developing world in Trieste, Italy. “This is a way to bring their work to the international forefront.” Nominations for researchers from 81 eligible nations who earned PhDs in the past 10 years will be accepted until 30 September.

Point the first: five people receiving $5,000 each is a pittance. Really? $25,000 is all you can muster? Come on, Elsevier, you've got to be bringing in more than that, considering the ridiculous costs of your journals.

Point the second: $5,000 will go a lot farther in, say, Burma than in Baltimore, but I'm sure there are other places on the list of 81 nations where $5,000 would get used up very fast.

Point the third: will $5,000 each to five women really be enough to "bring their work to the international forefront"? Somehow I don't think so.