Matthew D. Zimmerman, Ph.D.

This one I see quite commonly: the present tense of the verb to lead is “lead”. The past tense is “led”:

• “Our work lead to several results.” WRONG
• “Our work led to several results.” RIGHT

Why is this so confusing? It is probably due to the similarity of “to lead” to the verb to read:  namely, both the present tenses and the past tenses of the two verbos rhyme when spoken aloud. However, while the present tense “read” and “lead” are spoken (with a long “ee” vowel) and spelled similarly, the past tense “read” and “led” sound alike (with a short “eh” vowel) but are spelled differently.

This, I am sad to say, is one of the many examples of the very complex relationship between the way English words are spelled and spoken. However, the good news is that this behavior, at least for verbs, is limited to irregular verbs like “read” and “lead.”

Adverbs of frequency include words like “always,” “usually,” “sometimes,” “often,” “never,” etc. They are often misplaced with respect to the verbs that they modify. These adverbs come before the main verb:

• “The enzyme cleaves usually the bond when…” WRONG
• “The enzyme usually cleaves the bond when…” RIGHT

However, if the verb contains a derivative of to be, the adverb comes after the to be (and before the main verb):

• “The sulfonyl usually is deprotonated…” WRONG
• “The sulfonyl is usually deprotonated…” RIGHT

Restraints and constraints are often used in crystallography, but there is some confusion as to the verb and noun forms of these words. Namely, when using the terms as nouns, the “t” at the end of the word is necessary:

• “The restrains applied were…” WRONG
• “The restraints applied were…” RIGHT

However, the verb forms of the terms do not have an ending “t”:

• “The program does not constrain the data…”
• “We restrained the collected reflections…”

In which contexts does one use constraint vs. restraint ? Some scientists maintain that the two terms differ in meaning: namely, that a constraint  fixes a term in a refinement process to an absolute value, while a restraint maintains a term around a correct value via some sort of energy or weighting function (as used for example by AMBER). However, if you’re not (say) the developer of a refinement program, the terms can be used more or less interchangeably.

I work in a laboratory of about twenty people, and one of the few who was born in the United States (most of my colleagues are Polish, along with a few Russians and Chinese). Consequently, I read many scientific grants, manuscripts, and other documents written in English by people who speak it as a second language.

Recently, I began writing tips on the whiteboard in the lab correcting common mistakes made by ESL speakers, and it proved so popular that my colleagues asked me to put them online so that they might be able to use them as a reference. So this is where I will be putting these tips. I am a scientist—specifically, a structural biologist—and so is my audience, so some of the tips, such as today’s, may not be so applicable to a general audience. As well, many of the tips may reflect common errors made by Eastern Europeans, as these are the errors I most commonly see.

I hope that you find this useful, and I appreciate any feedback!

My dad wrote a guest opinion column for the local paper in Johnstown. Apparently Pennsylvania is considering legalizing video poker as a revenue-raising measure, and as the good Methodist minister he is, Dad is speaking out against it:

The legalization of video poker is a quick fix that preys on the citizens of Pennsylvania. Like any addictive behavior, it would trade a false and momentary sense that all is well for long-term heartache. We should insist on more socially responsible public policies.

See the article here.

Jonathan Coulton is one of those people that exemplifies the best of the Internet can be about. He’s a folky, slightly nerdy, and exceptionally talented musician who did the “Thing a Week” project a year or two, where he produced one song a week for one year and released all of them for free (under a Creative Commons license) on his website. Many of these tracks have subsequently battered geek culture like a series of class 5 hurricanes of humor, including an ode to lovelorn IT workers everywhere, the finest song about zombies ever written, and a cover of an 80′s classic.

So I downloaded the whole series of “Thing a Week” sometime shortly after the new year, and I like many of them a lot. But two songs in particular have stuck with me, not because they’re funny (they’re not), but in how they’ve really captured the tone of my life over the past three or four months: “So Far So Good“, and the ridiculously beautiful “When You Go“. It’s probably not a secret to the people likely to be reading this that a few months ago I was involved in a pretty bad breakup, which has been hurtful, painful, and messy. (I in particular said and did things of which I am not proud.) These two songs ring so true, one about what I’ve finally gotten over (“When You Go”) and one about where I am now (“So Far So Good”), that they’ve really gotten a lot of play time in my MP3 player. So thank you very much, Mr. Coulton; you’ve gotten me through a lot.

On Tuesday I successfully defended my Ph.D. dissertation, and am now a doctor (of philosophy in biophysics, so I’m afraid I can’t write you prescriptions). Those of you who feel that me finally finishing my degree after nearly a decade is a sign of the apocalypse (and at points I counted myself among your number) should make your way to the bomb shelters. My public seminar and defense went well, and I only have a few revisions I need to make.

Later that night, I found that my girlfriend Bonnie had thrown together a surprise graduation party for me in the church basement, helped by many other people. I was completely surprised. I kept saying I’ve never felt so smart and so dumb in the same day. Many of my friends, coworkers, and family were there, and some traveled a long way to be there. Leslie, a friend of Bonnie’s and mine, put up some pictures on her blog.

Thank you to everyone who came, and thanks to those who couldn’t make it but passed along good wishes. Extra thanks to my sister Suzanne, who put together a very nice (albeit mildly embarrassing) slide show and a wonderful scrapbook for me, my family for driving such a long way in a such a short time to be there the whole day, and to Leslie and Renita for helping to prepare the party and taking wonderful pictures. And of course, enormous thanks to my lovely Bonnie, who deviously masterminded the whole thing. I love all of you.

This has been a very long journey, and I’m so happy and relieved (and in some ways, a little sad) that it is over. I am so grateful for all of you who have walked with me at various phases of the trip. I couldn’t have done it without you.

In case you may be concerned that I have fallen off the face of the earth, I’ve been working on my Ph.D. dissertation. But I am emerging from my cocoon now, as yesterday I turned in my dissertation to my committee. (Yes, this has been a long time in coming– cough, cough, nine years, cough…)

My defense is scheduled for Tuesday, September 18, 2007 at 1:00 PM. I will give an hour-long public presentation of my research, then my advisor and the four other faculty on my committee will shepherd everyone else out of the room for a closed-door oral examination. If all goes well, they will sign my cover page and I will be a doctor. (No, not that kind of doctor.)

The presentation is open to the public (if you are in Charlottesville, it will be held in the large conference room on the fourth floor of Jordan Hall) but I suspect that unless you’re a structural biologist, you would find it pretty dull. There will be some sort of celebration to take place that week, so stay tuned.

I wrote my last “A Year In The Life” column for the Wesley Word, the Alumni newsletter for the Wesley Foundation, and I must say I think it’s a good one. As not to steal their thunder, I’m not going to reprint it here until the newsletter comes out.

Incidentally, it’s much, much easier to write about a trip to Beijing, which is what the last one was about, then about writing my dissertation, which is what this one (and my entire life at the moment!) is about. Just sayin’.

God, I hate pollen.