Wednesday, August 26, 2015

Before there was the first, there was the second

Note: this post is not [directly] about science, but about the family I grew up in. Sister and I are thinking of writing out some of our family stories. It might make a good children's book.


Many years ago, while we were a little bit younger, but already scattered to our adult lives, I got the call. “Sister—The second-worse fate that could befall Father has now come to pass.” I was flooded with visions of amputated limbs, or fathers at the bottom of the well, or the lake—but surely these are examples of the first-worse-fate, right? And if so… what could be the second?  “”Wha…wha… happened?” I think I might have said. “Mushrooms,” said Sister. “Bad mushrooms.”

This I understood immediately. During our childhood, Father led mushrooming trips any chance he could get with Sister and me dutifully tromping behind in the woods. Father would hunch down next to a specimen, the glossy, heavy-paged Audubon Society identification book in hand, muttering: “‘choice, edible?’ Or ‘toxic, poisonous’?” Then Sister and I would cringe together as Father took a small test nibble.

Mushrooms also appeared later*, after they had taken on additional meanings. During these post-college days, one or the other of us would get a chance to visit Father, and share the north country adventures over the phone with the other sister, stuck back in her normal life. Once, in the midst of an intense series of synchrotron experiments, I got a call from the ADKs, and there was no small talk:  “Burr [childhood nickname]--We have just eaten a pile of mushrooms we collected earlier. We are over 90% sure they are ‘choice, edible’ but there is a small chance they are ‘dangerous, hallucinogenic’. We sautéed them in butter, garlic and ‘herbs’ and they are delicious. If we don’t call you back in 30 minutes, then call Nick and Tammy up the hill. Bye.” Click. Yikes.

Sister and Father called after 30 minutes to report no physical or perceptional incident. And Father also survived the second-worse-fate-to-come-to-pass, which probably happened when a bad lookalike was collected along with the shaggy manes. It only caused about two days spent more dependent on indoor plumbing than Father is accustomed to. 

And the first-worse-fate? Well, I don’t yet know how it ends, and I might not be the one to best recount it. And in the end, the scenario ordering is subject to re-arrangement. Only Father can say which was actually the worst, during the living of it.

* Am I allowed to write: “Mushrooms appeared sporadically.”?

Monday, June 15, 2015

Almost Binary

I’m working on a research problem dealing with numbers that are either close to unity or close to zero. So much so, that the mathematical training and practice that I’ve had up until now would not allow me to do this problem. Indeed, in several iterations, I have done pages of derivations that end with a trivial result 1=1 or 0=0. (1=0 means that I have made a very different type of mistake).

So much my time recently has been spent trying to avoid triviality.

As I’ve been working on this problem, I’ve been inventing math, and it blows my mind with a sense of discovery. Then I look it up, and it turns out that it has been discovered in 1760. A shout-out to all of you mathematicians on Wikipedia: Thank you so much!

Notes to self:
2. Make friends with a mathematician

This week it’s averages.
How do you take the average of two numbers, A and B?

1/2(A+B) or (AB)^1/2
Arithmetic mean or geometric mean?

These numbers will be different: am1 and gm1.

But then you can take the arithmetic and geometric mean of am1 and gm1.

½(am1 + gm1) = am2
(am1 x gm1)^1/2 = gm2

and keep on going and going and eventually the answer will converge. That's the arithmetic-geometric mean.

I’ve been playing with this for a while, but I just discovered that Gauss had already been playing with these probably close to 200 years ago.

For me, doing math is meditative, lovely.  I am fully concentrated on the abstract, far from the world of people & feelings & things I have to do.

Here is a partial recording of the part of my brain that is not re-doing 200-yr-old math.

1.     Um. Is this a good use of my time?
2.     How could it be bad for me if it’s so much fun?
3.     Now I understand how to derive things
4.      Omigod I’m sooooo sloooow
5.     I suppose it’s a better use of my time than other things I can be doing
6.     But perhaps not a better use of my time than other-other things I can be doing
7.     In the end I really really want an elegant solution to this problem and I know I’m almost there.
8.     Keep on plugging.

Sunday, March 1, 2015

Please Ask Permission

Back when my child was still at the age where he had a great deal of access to my body, when he felt like it he would simply reach out and touch and/or hold my breasts. For a time this was obvious, natural, and welcome. Then for a time it was just fine. Finally came a time when it was not fine anymore, especially in public.

I called a meeting of my motherhood-cabinet—my wise friend Alisa. We discussed the issue: it’s time for me to teach him that he cannot grab my breasts at will. But I don’t want to tell him “he’s not allowed.” Because he is still allowed to touch me, and I want him to feel allowed in the future. Allowed, but not entitled. We laughed a lot, especially while imagining his future relationships which felt impossibly far away, talked about it, and she helped me hatched a plan.

The next time my son grabbed my breast, I took his hand, gently moved it away from me, and told him: “You may touch my breast, but only if it’s ok with me. You need to ask for my permission first.” My son looked at me, and reached again to touch my breast. Again, I took has hand, moved it away, and said “My breasts are private. You may touch them, but only if it’s also ok with me. You need to ask people first before you touch their bodies.” My son went back to play, life moved forward, and I forgot.

A few weeks later, we were waiting in the crowded Saturday morning Wegman’s checkout line. From his seat in the grocery cart, my son asked me in his clear voice that seemed to cut through the entire busy grocery store: “Mommy! May I please touch your breasts!?”

Moral of the story: Think through your entire plan, not just the first part.

Thursday, February 5, 2015

On Derivations

How to derive things:
1.     Start with a good cartoon
2.     Consider the simplest approach to the physics
3.     Be clever in choosing your reference frame
4.     Add numbers to your cartoon
5.     Do the math and/or arithmetic
6.     Iterate as necessary until doable and obvious after-the-fact

At some point in my academic career (college? grad school?) I decided to get serious with my studies, and build a habit of going through derivations, step by step, with pencil and paper, in order to understand.

It is an only an occasional habit, part because of laziness, but also because if I spent my time walking in detail through every derivation, I didn’t feel as if I would have enough time left for my other activities.

One learns a lot of researcher shenanigans going through derivations. Be wary of the line that says something like: “We can obtain equation 3-9 from equations 3-5 through 3-18 and application of algebra.  If you want to do the algebra, budget yourself many hours-days-possibly even weeks.

And then there are the assumptions. What if one of them is wrong? How does that change the derivation? You can almost guarantee that the assumptions were required to make the problem doable for the scientist.

The first thing anyone should know about derivations is that they often seem obvious in retrospect, obscuring the combination of inspiration and perspiration (and frustration) that was invested into the derivation.  While a nice derivation is neat and tidy and perhaps a little bit exciting, the process the scientist (more likely: scientists) took to do the derivation was most likely totally messy, filled with wrong turns, and dead ends, and endless frustrations.  The derivations are the stories that are told after the real life has been lived.

In my scientific life, I have derived one new equation (Kavner et al., 2005, eqn. 12). It definitely ranks up there as one of my top life experiences.  It took about six weeks of work (most days, from 8 in the morning until lunchtime—at my desk with pencils and a stack of paper) to cover enough wrong paths and make enough simplifying assumptions so that I could complete the derivation in one sitting.

It was so much fun that I’m working on another, more complicated one that generalizes the first one and fixes some of its problems.  This one I’ve been working on for far longer—on and off for a few years. I promise I’ll share it when I’m able to.

In the meantime, here is an annotated derivation of the Hugoniot-Rankine shock wave equations. The derivation is from a combination of Poirier’s textbook: Introduction to the Physics of the Earth’s Interior and my notes from my PhD advisor, R. Jeanloz. Annotations are mine.

Wednesday, October 1, 2014

Favorite Journals

One of my postdoctoral advisors had a policy about manuscript submissions: when he felt he was treated unfairly during the editorial process, he would refuse to submit to that journal again. You can imagine that high-profile journals had been long eradicated from his goto list. In fact, towards the end of his career, it is almost true that the sole journal left for his submissions is Canadian Mineralogist.  High quality journal, but limiting.  One of the many things I learned from this particular advisor is the value of not holding grudges—in the realm of scientific publishing of course, and more generally too.

The Journal of Applied Physics has a special place for me and I think for many in my field of high-pressure mineral physics.  While many of us are geophysicists, and mostly publish in Earth sciences related journals (and I have some favorites in that category too) we are also materials scientists and condensed matter physicists. Materials are neat, and even more so when compressed and heated to extreme conditions. There are interesting applications for high-pressure and -temperature research (hint: KaBoom!). And identical concepts and tools are brought to bear on the materials we study—mostly oxides and metals. If I have a contribution in applied materials physics, that is not PRL-level groundbreaking, then I often submit to JAP.

            Recently, a collaborator and I finished a tightly written manuscript on the high P,T behavior of Co metal. My assessment: technically challenging experiment, nice data, interesting analysis, useful for us and others, but not groundbreaking.  JAP is the perfect venue for this. JAP has published papers by others on the same material, and papers by me describing simililar measurements using similar methods on other materials. But yikes! When we went to submit, it appears that our contribution does not fit neatly in any of the available subcategories for manuscript submission.

The story ends happily. I sent a polite email to the editor-in-chief, asking if the intention is to exclude my field from the journal, and he responded quickly and favorably, saying no! Definitely not! The only intention was to modernize the table of contents, but not to exclude, and politely requested my input on how to refine the table of contents. The manuscript is submitted. Wish it well!

Web-of-science search of JAP plus "diamond anvil cell"
Web-of-science search under my name plus JAP.

Friday, August 29, 2014

Trail Names

This summer, my son hiked the entire Green Mountain Long Trail with a group of teens from his VT camp. Putting aside the naches-induced kvelling for now, I want to write about the concept of trail names. These are nicknames that long-form thru-hikers bestow upon each other (no-one gives themselves a trail name) that simultaneously celebrate their journeys and acknowledge the difficulties of the trail.

Some examples from my summer travels…

Holly Hobby (curly red-head/freckles)
Mister Blister (AT thru-hiker with crocs & duct tape as footwear)
Little Turkey (A kid that I know, who was spooked by a bevy of flapping grouse)
Left It Burning (don’t forget to put out that campfire!)

Summertime is wonderful, isn’t it? Wasn’t it?

And then there is today—there is my friend and colleague Hope Jahren’s blog post about a deranged colleague mis-sending her a nasty email full of vitriol. (I recognize and point out that the colleague's idiot actions have absolutely nothing to do with Hope at all. I hope that Hope’s chair/dean does the right thing and has an official notice placed in this person’s personnel file and insists that he obtain what appears to me to be much-needed psychological counseling. Dear Hope's Chair: Compulsory counseling is a thing. Use it.)

Hope's story shocked, saddened, and horrified me. And reminds me of my own experiences, many years of observations, and all of the other stories I hear from the women in science. Part of me wants to bury my head in my work and block out the mistreatment of self and others. Ignore it, hope it goes away, try to keep moving forward as positively as possible while looking for opportunities to promote change from within. After all, any criticism about my science is welcome—will only make my science better and me a better scientist. The psychological work that must be done to keep my keel down and sails out—that can only serve to make me a stronger wiser and hopefully more compassionate person.

The unfairness of it all— the discrimination of women in science at all scales, not just sensed and observed but documented in so many places, in so many ways—it’s real. It’s here. And it is in addition to the “normal” stresses of the job that we all have as scientists, including more  uniformly distributed generalized unfairness (perhaps this should be called the “non-gender-biased component of unfairness)—like the scramble for scarce resources we all must participate in, and the generalized lack of professionalism in the academic environment.

This needs serious counterbalance. How many attaboys make up for each awshit? 

I will tell you that my own personal professional requirements are consistent and humongous helpings of wonderful science with my days filled with data, discussion, working, and writing with a multitude of diversely talented, intelligent, clever and committed people.

My Vision:  We Female Scientists create about ourselves and our departments and our intellectual communities wonderfully rich and rewarding days, with immense intertwined systems acting to support all of us--women and men and research staff, undergrads, faculty, admin, grad students--as we continually push ourselves and each other to do our best science and be the best scientist-citizens we can be.

We need trail names, don’t we?

It might be small and simple but maybe a powerful way to share and celebrate the journey we are on as scientists while also affirming the nature of difficulties we encounter as female scientists on the trail.

So I’ll start the ball-rolling by suggesting:

Hope Jahren: Warrior of the Growing Life

Wednesday, June 25, 2014

Goldschmidt Conference Report-A Blog-Along Conversation

I just discovered Terry McGlynn’s great blog, and he wrote about a geochemistry conference—the Goldschmidt conference—which I attend occasionally. I was there in Sacramento, and I’m sorry I didn’t get to meet you, Terry. Here, conversation-style, are his comments and my response & discussion.
·       As far as I can tell from this conference, if it were not for the study of isotope ratios, we would know absolutely nothing about the earth of the Earth. There’s a scene from Being John Malkovich in which all characters just say, “Malkovich, Malkovich, Malkovich, Malkovich.” This meeting felt similar: “isotope, isotope, isotope, isotope.”
True—but remember that “isotope” is a tool (it’s just chemistry, after all, on an extended periodic table) and the scientific questions-and-answers are key.
·       A lot of geochemistry is about developing and assuring the validity of methods. It all comes down to the accuracy and reliability of methods. I’d say that the vast majority of the talks and posters that I saw were about methods.
This community is heavy on the methods-development. This is good—there is great scientific richness to follow when better & better methods are being developed. Perhaps the focus on methods-development is an indicator that the science itself is not overly-mature.
·       A not-uncommon conversation-starter: “What machine do you have?”
“How big is your machine? Mine is so big!”
Such an interesting conversation to me because I come from a community (mineral physics) where we have made the transition to shared community resources for much of our work. I prefer the term “evolved”, and many years ago discovered that I could really make a geochemist uncomfortable (if desired) by saying the words “Shared community resources”
Much of the state-of-the-art mineral physics measurements are made at synchrotron-based beamlines, which are one to three orders of magnitude more expensive than mass spectrometers, depending on how the accounting is done. What this has meant for our field is worthy for an entire post, but includes at least these four positives: 1. Shift in focus from the techniques to the “big science questions” 2. a semi-organized community effort to discuss grand challenges and seed community infrastructure and facility 3. the ability for mineral physics to exist at smaller institutions, not just large rich ones. 4. More camaraderie and cooperation in the early & now-approaching-mid-career generation than in our previous pre-synchrotron advisors’ generations.
I think at least partially adopting this model would very very very (x100) good for isotope geochemistry.
 Geochemists are beardier than ecologists. But perhaps less scruffy.
Is the gender balance similar? Are there more beards simply because there are more men?
·       When conference registration costs about what I imagine you could get for a kidney on the black market, you get what you pay for. Very well organized, copious snacks of the non-cheap variety (including fresh raspberries and blackberries) and always fresh fruit available, constant coffee, and lots of drink tickets for the poster sessions. Which serve good beer. (Then again, the Entomology meeting is only one hundred bucks cheaper or so, and they don’t have any of that). And the students who volunteer not only get free registration, they also get paid!
The student-volunteer aspect is a good reminder for those who kvetch about costs.
·       I’m used to ecologists battling for fame and status by being the champion of an Important Theory. At least from the view of an outsider, I didn’t see this so much of it in Geochemistry. People weren’t selling theories, they were selling methods. (Then, I was told by insiders, once a method is unassailable, then it can be used to make all kinds of claims.) There still are crazy politics and personal agendas, but from my perspective, this meeting seemed a little closer to the false stereotype of the careful and passionless scientist.
Don’t worry! Grandstanding abounds!
·       These folks are, on average, fun and laid back.
Aren’t first impressions great? My guess is we’re the same…

·       Geochemistry has the same ethnic diversity problem as the fields of science with which I am familiar. And maybe a little worse.
Insert frowny face here. Note: perhaps existence of some community resources  will help diversify the field? Not sure if it has or has not for my field.
·       I was surprised to not see a super-duper emphasis on over-fancy statistics. There was plenty of modeling, and of course a well-reasoned treatment of variance and sampling errors. The approaches to stats were definitely not shoddy, but lacking the statistical machismo that I’ve grown accustomed to among ecologists. I walked away from the meeting with even greater confidence in our stated understanding of the historical chemical conditions on the planet.
Interesting—I think those with extra-worthy statistical chops can clean up in certain areas of geochemistry. Also big-data approaches might be useful.
·       When insect abundance increases in response to nutrient availability, then this is best summarized by saying that insects are “indicators” of nutrients. (To me, that’s a little bit like saying that a delicious meal home-cooked meal is an indicator of a quality grocery store.)
Oops—did someone misunderstand one of the points in your talk?

·       I suspect it’s harder to be a geochemist at a smaller institution than it is to be an ecologist. Geochemistry seems to always require one or more expensive machines that require constant love and maintenance. (This machine apparently measures isotopes of some kind, in some way.) So, you first need the cash to have the machine, and then you also need to keep a full-time lab tech. Without a tech, then faculty end up being mechanics rather than manuscript and grant machines. I suppose fancy private colleges can keep machines running if you’re blessed with a good technician.
·       You’d think that geochemists get to tramp all over the world for fieldwork. But from what I could tell, a bunch of people work locally. Moreover, a bunch of people are relying on samples collected by others. There is plenty of fieldwork; I talked to a grad student whose thesis is about dating volcanos and glacial periods in Iceland. I met a really cool guy who’ll be spending time working in super-remote Siberia. And people who go scuba-diving on coral reefs. But, it seems like a lot of it is in the lab, based on core samples that someone sends to you in the mail.
See my response about shared community resources. They permit participation from a wider variety of institutions. Less focus on instruments for some scientists means more focus on questions & science & samples = better geoscience.
·       Every person was extremely generous with their time in explaining very basic things to me. There were many terms and acronyms that they knew that I didn’t, and basic mechanisms or analyses that I hadn’t seen before. And big theories too. Bigwigs, postdocs and grad students all were both interested in sharing with me and took their time to make sure that I really understood what they were doing. I had the opportunity to ask a bunch of questions, and I did far more listening than asking. It was refreshing that this non-specialist was not only accepted, but also welcome, at the conference.
I found the same to be true (in general) when I first started doing isotope geochemistry experiments. There was some hostility, but balanced by support.  
·       What a bummer that it was in Sacramento this year. Vienna would have been nicer.
I have the opposite opinion about this. I liked the fact that I could drive to my state capitol, rent a cottage a few miles away, and bike back and forth to the conference.  Vienna—especially—is one of my least-favorite cities I have visited.
·       I met some folks at the meeting who I know internet-knew through this site, and they were really cool. I also failed to cross paths with some people, too, since I was only there for a short time. And since there are presumably a few geochemists reading this now, they’re well prepared to correct my misconceptions, I hope!
I’m sorry I didn’t meet you in Sacramento. Looking forward to meeting you at another Goldschmidt conference