Friday, August 29, 2008

Parameter check

I was working away this afternoon, continuing to wrestle with a sticky problem dealing with numerical differential equations solutions in my model – an issue that has ultimately been underlying much of my difficulties for the last several months likely. Sometimes, however cleverly you program something, numerics just won’t do the trick, as a problem is too hard or too picky to small errors. Talking about this problem with my adviser resulted in a sort of reality check, which I prefer here to think of as a parameter check, since I’m skeptical that what we do is easily related to reality. Turns out that making the parameters of the model much more akin to the actual limitations of biological reality seems to shift the functional forms into something much more easily and accurately resolved by numerical solution methods. Poof. Just like that. Most everything runs more smoothly, accurately and rapidly in this different region of parameter space. So that’s nice.

I mention all of this because it’s a nice new development in my project, but more significantly because it sort of book-ends a train of thought I’ve been bouncing around in my head this evening. I guess I’ve been reality checking science and my motivation and participation in it. Part of this train of thought is also attributable to a book I’ve just finished reading, “The Immense Journey” by Loren Eisley, an anthropologist, naturalist and scientist of the last century. The book was published in the 1940s, and Eisley himself passed away in the late 1970s. In this book, he covers concepts of evolution and scientific history as applied to the origins of life from matter, and humanity from other life forms. He talks about both early scientific theories, and how they changed through time, leading up to ‘current’ understandings. And now ‘current’ is some 60 years later. We have a lot more information drawn from paleontological findings, improved dating techniques, and advances in genetics and biotechnology. Some of this information provides answers to the conjectures Eisley made, and not always confirmation at that.

So we have a better, or at least more complete, story to tell know about the origins of life, how it changes over time, and how we are connected to it. And it strikes me that quite a lot of science is like this – a detailed story seeking to explain sets of observations made about the world. But that’s not all – as I’ve been observing this summer, a great deal more accompanies this purported goal of science, consisting mainly of hoops that have to been navigated successfully in order to secure funding, publish journal articles, obtain and maintain collaborations. This is stuff that you don’t hear about as often as being a major component of a scientist’s job – they’re just the pasty, safety goggle, lab-coat sporting, caffeine addicted, more or less nutty and socially inept people permanently on the verge of major breakthroughs, right?

I’m feeling a little jaded about science and my participation in it currently. Reading historical accounts of science, I’m given the distinct impression that just a few decades or centuries ago, there were major questions facing science – questions rather clearly defined and sources of great mystery, which inspired heroic efforts and intellectual feats on the part of the towering scientific figures we know and love… Mendel; Darwin; Franklin, Watson and Crick; etc, etc. (being most familiar with biology, I’ll stick to examples from this field, knowing that similar things could be said of other disciplines). Important theories regarding the processes governing the changing tapestry of biological life generation to generation were secured. So much of the work done since the formation of these theories has consisted of case studies illustrating the successful application of these theories to various and sundry biological systems and organisms. But where are the big unknowns, the big mysteries remaining to be answered, without which nothing else quite makes sense? I feel like they’re not there. Or if they are, they aren’t nearly so well defined and acknowledged as the mysteries of previous eras. It seems to me that right now, the bulk of scientific work is concerned with tidying up all of the details left behind in the wake of these theories. Figuring out how they act in a plethora of different systems, many of which, granted, have fascinating quirks and intriguing features.

But where are we headed? What is next on the horizon? What questions loom unanswered, and what are the necessities which drive us to find their solutions? Where is science taking us? Are we at the point where we’re pushing beyond the realm of realistic pursuits (‘parameters’) into regions of greater difficulty and little return? Should we pause for a while, reflect on what we already know and the significant challenges that we already face, and say to ourselves “Wow. Maybe we know enough for right now. Maybe we need to spend more time making use of our knowledge to change the way that we live and our society operates, if we want to stick around and maybe someday have the leisure to seek out new questions”. It just seems like at some point, if we don’t pay attention, the juggernaut of science will come to a crashing halt, as we realize that for all of the data and theories and papers and presentations we’ve amassed, we never paid attention to the important things that we already knew, back when there was still time to put knowledge into practice for good. Fanatically struggling to pin down the last little details, will we forget to pay attention to the broad messages already known? I guess this is the balance between the pure and theoretical and the applied and messy business of practicality.

Maybe it’s arrogant to think that we’ve solved all of the major mysteries we’ll face, or maybe it’s a factor of youth and inexperience. But I think the balance that it highlights between considering the important allocation of effort to theory AND application is really worth some thought. Certainly it’s a question that has been giving me some trouble, as I do a lot of theoretical work, but in looking back, what drew me to science originally was the application – the part where you do things and touch things and see what comes back at you. And in particular, the part where your actions have a tangible, perceptible and positive influence on the world. Having spent the last three months of my life living as close as I ever have the lifestyle of a scientific researcher and theoretician, able to focus intensely on research, I feel that all my work and theories and progress don’t mean so very much in the end. Yeah, I know it’s only 3 months of work. But I feel like even if I were to answer every last little question I have about the system I’m studying, the sum and total of those results still wouldn’t mean anything in the end.

Partly I think this is a function of the tendency in science now for research resulting in a paper or grant funding to arise from the ability of a scientist to sink deeply into academic literature, and then dig a little hole – the narrower and more specific the better. From that hole, we dredge up every last thing we can find, until we become the unquestioned experts and lords of an almost infinitesimal domain of knowledge. And this forms the basis of a successful academic career. And this is the kind of process I’ve been participating in for at least two of my three ongoing areas of research. Productive – yes, in a career and academic sense. Meaningful – you tell me. The only people I can even talk to about what I do in anything but the broadest terms are immediate members of my lab, my adviser, or maybe a field of a hundred academics most of whom I’ve never met nor interacted with.

One year later, I’m still wrestling with the process of applying to graduate school. I think a major part of my challenge here is that a part of me is really rebelling against this tendency towards specialization. If you have a passion for a narrow topic, choosing a graduate school, discipline and adviser all become much more straight forward. I, with my general curiosity, and increasing distaste for extreme specialization, am finding it very hard to identify who I’d like to work with, because each faculty adviser has their own subject niches. I feel like once I choose, I’ll be pigeon-holed.

So what should I do? Choose to play the game, pick a grad school, adviser and a topic and dive in? Is it possible to remain general, to keep an eye on the general directions of an entire field in a critical and significant way and not get lost in minutia? If I dig myself a nice, tidy academic hole, beyond the ‘success’ that that path could bring me in the context of my field, am I still being useful and doing worthwhile things with my life? Certainly that’s what a lot of people would like me to do, and they seem to think I’d be quite good at it. Or should I check out, say so long suckers, and start participating in actively changing the world, implementing what we already know about how we need to change our lifestyles and communities to become environmentally sustainable? It seems like I could keep feeding the driving curiosity that first brought me to science on the vast libraries of things that are known for the rest of my life and still leave so much unlearned. Would that be satisfying enough for me, especially if I were able to lie down to rest each day able to say “Well, I tried to change the world today. That’s something.”?

This has turned out to be a rather enormous post, but it’s been brewing for a while now. Kudos if anyone read it all. If you did, I would really love to hear what you think – this is a little out of my normal style, but these are things I’m seriously thinking about and don’t have answers for. I know for sure that at least two of the maybe three people people total who read this blog are involved in science in varying ways. Any thoughts guys?

Wednesday, August 27, 2008

A day in the life of Transient Theorist...

Again, quite a lot has happened since the last time I wrote. I usually prefer writing in the evenings, and the house I've been living in the last two weeks or so doesn't have internet. For a geek, this is a serious matter - see xkcd comic via Aspiring Ecologist. I guess this means I can no longer deny my geekdom.

Life has fallen into a routine here again, although things are about to get shaken up again, more on that in a second. Most days I rise before 7:30, pack a lunch, and ride a borrowed bicycle a mile or so into the lab here. I wasn't sure I'd like it, but I think biking to work everyday is great. Much of my days are spent sitting in front of a computer - it's really nice to move some in the morning and get my heart rate up before settling in for work. And in just a week and a half I've already noticed that the commute is a lot easier - my legs hardly complain any more. It's starting to get cool here though - I definitely appreciated the sweatshirt I wore for my morning ride. I frequently see deer in the agricultural fields I pass every day. They don't seem to know quite what to make of a funny looking guy on a bicycle. All in all, I think I'd enjoy situations where I bike into work in the future. It is pretty frustrating in such a rural area to try to exist solely on bicycle though - I hate asking other people for rides to the store and such. Even if they don't mind, it still bothers me. And trying to plan out things carefully enough that I have everything I need for the foresee-able future is kind of stressful. The store is just too far away to ride to, although I have found a small local market over by the lake where I could pick up essentials if I need to at some point. I'm very please with the rack on the back of the bicycle I'm using - my own bike back at my parents' house doesn't have a rack. This thing easily and securely fit my entire bag of dirty laundry and detergent!

After making it to work, usually I toast up a bagel in the toaster I found upstairs near the administrative offices, and then wander the internet a bit while munching on breakfast. Research/computer work until lunch around noon, then several more hours after lunch. Still playing pick up soccer twice a week, although the last several games have been quite sparse on people, resulting in lots of running. Most nights I'm here until at least 8 pm, jumping on the bike in time to ride back to the house I stay at before it gets dark. After riding home in the dark one night earlier this week, I decided that, while exhilarating, it isn't something I want to make a habit of. Back at the house, I make up some dinner, and then read or talk on the phone until I fall asleep.

Right now there's only one other person living in the house - a temporary residence for people visiting the station. It's possible that he works more than I do, so I rarely see him. I've never met someone that eats sooooo much fish - pretty much every meal I've ever seen him cook involves chunks of fish, fennel, green onions and some combination of vinegar and soy sauce. Not sure what to make of it, although it's making me sort of paranoid about wiping down counters and dishes an extra time or two. But yeah, all in all, it's really quiet and a little lonely here right now, in comparison to earlier in the summer when all of the summer research students were here and I lived on campus.

I guess in one sense though it's in keeping with some of my goals for this year off - I'm definitely challenging myself a little after being so used to living with friends on a college campus and seeing loads of people every day. I've definitely always been pretty self-sufficient in terms of being able to look after myself, cook, clean, make decisions and the like. But I'm getting the feeling that this is sort of a new kind of self sufficiency that I'm tasting in a small way - figuring out how to depend only on yourself for company, a sort of emotional self sufficiency. Certainly this is a mission that historically many thinkers and naturalists embarked on, from Thoreau to Abbey and the like. I almost think it would be easier their way though - jumping out into the wilderness, and forcing yourself into a pretty total isolation, instead of being partially disconnected from things. With this partial disconnect, you're still frequently made aware of the small separations that have been made and the things and people that are missing, sometimes in unexpected and emotional ways. Hard to say for sure though, unless I set off on a more severe solo experience for comparison's sake. Looking back on my life to date, I've never really been alone quite like that. Maybe I should try some solo camping/backpacking(?).

Research itself going quite well. My adviser has been significantly impressed by what I've shown him the last several times we've met. The programming language I've spent the summer learning - Mathematica - is really starting to feel comfortable, which means less frustration and more productivity for me, although I still have lots to learn. One thing that struck me today, after talking with some of my friends who are starting up fall semester, is that I can do research all day (10-12 hours of it often here), and my head never gets to the point of numbing, blah tiredness. Don't know why this is - maybe all that brain-stress I remember from previous years derives from those days where you've got 4-5 classes in unrelated subjects and you have to keep switching gears, whereas with research I just keep thinking about the same sorts of things most of the time. Beats me.

Upcoming in posts in the next few days - news on a new job I'll be starting soon (continuing my transience), books, more from the writing a journal article saga, and maybe transportation/housing. Fascinating. But I'm being encouraged to go home and cook dinner at a normal hour, instead of waiting until 8:30...


"When we have found all the mysteries and lost all the meaning, we will be alone, on an empty shore."

"Then we will dance."

- Tom Stoppard

Monday, August 18, 2008

Yup, I'm still breathing.

Ok, so I know it's been ages since I posted. What can I say? Life's been busy.

ESA went well, all in all. Didn't muster up the gumption to talk to as many prof's as I had intended to, but I did listen to a lot of their talks and talks given by their students. I also picked up a couple of new names to look at for grad advisers. The more enjoyable part of the conference was meeting up with friends I hadn't seen in ages (at least a year for some of them), to catch up on stories and adventures, as well as meeting their labmates and friends. Also, there was a fantastic book store - I barely escaped with only 6 books, feeling rather accomplished.

All last week, Bait was here visiting - it was awesome! Hadn't seen her since the end of May, eek. These long stretches suck. We had a good week though - hanging out, playing in/around the lake, going for walks, checking out some crazy birds, eating meals cooked in a tiny kitchen, watching the summer Olympics, and such. I took some time off from research, and felt no guilt about it (I felt justified, since I worked M/T, and none of my labmates returned from ESA until at least Wednesday... that and I was between grants last week, so I wasn't getting paid). When I did work, I pushed forward on my manuscript. Making definite headway, for sure. Discovering a new database system opened up a wealth of relevant papers I hadn't come across before. This was both exciting and frightening, as many of the pieces of my own rather original project have apparently been studied in isolation already. Time to get this baby out the door!!!

After taking Bait to the airport this morning, I packed up all of my stuff and moved to a temporary graduate student house just about a mile from the academic buildings here. It's a lot cheaper than where I was staying, and I have to pay for my housing now. It's going to take some adjusting to though - no TV (who cares), but also no internet!!! Gasp. I'm going to feel like I'm missing an arm or two. I forsee spending a lot more time here in the lab working in the evenings and such... Maybe this will increase my productivity. I'm hoping the lack of internet at my place will be a good thing - it opens the possibility of reading more books, writing some snail mail and such. I guess time will tell. Mostly I think I'll miss chatting with my friends in the evenings on aim.

More things to say, but I'm getting hungry after a very busy day, and I still have to unpack and organize all of my belongings back at this new house... time to hit the road I guess.

Take it easy out there people.

Tuesday, August 5, 2008

Reporting in...

So I'm at ESA. Probably close to the busiest week of my year - today I was gone from my room from about 7:30 am until almost midnight. Days are a whirl wind of scientific talks, rushing between rooms, talking and meeting with friends/aquaintances, trying to remember names and schools and disciplines and research topics and advisors, working up the nerves to talk to well known people about grad school, squeezing in meals on the go, wandering the exhibition hall looking at posters and vendor displays, and even this morning spending 30 min interviewing for a field job.

This is all both exhilirating and exhausting, exciting and emotionally draining. I'll have more to say either later this week or next when I have the time again. As for right now, Ecology pretty much owns my life, for better or worse. Previous years weren't this hard, but since I'm job hunting and grad school hunting, I've got a lot on my plate. Thank goodness I'm not presenting! A layer of stress i don't need right now for sure.

Ok, take it easy. I'm gonna crash for a few hours before it all repeats again.

Friday, August 1, 2008

Good news + updates

Ok, so if the last several postings have seemed a tad too much on the emo side of things, my apologies. I've never kept a consistent long-term journal before, usually when I write in a journal style it's because there's something significant on my mind, or something troubling me, and I write to sort things out for myself. So I guess that's sort of the default voice I've been adopting recently, especially since the last two weeks have been fairly high stress.

But just to show both (?) of you that I'm not always like that, this should be a pretty up-beat post.

So in the last five days quite a bit has happened. Monday morning I was informed by "Seahorse", the director of the summer research program that employed me up until today, that on Wednesday I'd be giving a 20 minute talk on the research I've been doing here all summer with my mentor here. Although I sort of suspected this would happen as 'Seahorse' and I had talked about it several weeks ago, this still induced a little bit of panic, as I still lack significant results from a summer's worth of work, even though I haven't exactly been twiddling my thumbs. Fortunately, to even explain the few results that I have at this point required providing a lot of backround material on the mathematics underlying my work.

While it was challenging to figure out how to provide this backround to my audience, several of whom had very, very little mathematics experience, in less than 20 minutes, I really had quite a lot of fun putting together a powerpoint with some humor in it, and carefully thinking out how I would try to teach material that it took me several weeks to teach myself back in June. That took up most of Tuesday, until rather late at night. I had enough time to practice it once in the morning before the session of talks began (all of the other students in my program were presenting as well, although for them it was part of a class project).

"Seahorse" made home-made donuts and brought them in for the talk session - they were awesome. I had two of them while sitting through a series of talks of varying quality (some of the statistics presented were frightening, in terms of the miss-use of statistical techniques and the invalid conclusions that were drawn. Biology students tend to have a very poor grasp on statistics, frighteningly. But I won't rant about that now). The talks all went long, and most were followed by quite a few questions, so by the time all of the regular students had gone, we only had ten minutes left before lunch started in the dining hall. Figuring that I was safe and wouldn't have to talk until after lunch, I snagged a third donut. Just in time for Seahorse to tell me to go ahead and present, and to try not to take too long. Throwing caution, and sadly my donut, to the wind, I launched into my talk.

And it went really very well. Quite a few people afterwards told me that I'd done a really good job explaining everything, and that they had found my talk interesting. One of these was the director of the entire biological station where I'm working/staying - really exciting. I even managed to answer the question she asked me at the end of my talk in an intelligent manner, drawing in part off of a point that another visiting eminent lecturer had made in a talk the previous evening (yeahhhh!). I was especially pleased though to hear from some of the other students that they had understood my presentation well; I want to be a teacher someday, so it definitely makes me feel good to know that I'm learning how to lecture a little bit (although I know that as a prof. I won't have all day to prepare for a 20 minute lecture, which will challenge me for sure). The only disappointment was that my mentor for the summer didn't make it to the talk. :-/ I always feel like we never quite connect when we're talking, and would have liked the opportunity to demonstrate to him that I really do understand what I'm working on, and such. Oh well.

With that out of the way, I switched back to working on my old paper. By now, I'm pretty sure that I have a brand new draft to share as a surprise with my old, amazing advisor/co-author from my college when I run into him next week at a conference. Things are finally starting to fall in place there. I've chatted a little with Seahorse about it too, and those conversations have been helpful.

Spent some time tonight relaxing (swimming, eating, swimming, cherry pit spitting contests, eating, volleyball in the half dark, etc) with the other students in my summer program, as the majority of them are leaving tomorrow :-( It's been a real fun group of people by and large, and I will be sad to see them go. It'll certainly be a lot quieter here after i get back from the conference next week. Several other students from the station here will be at the conference though, along with some good friends from previous years, so that takes a little of the sting out of things.

I've managed to secure transportation to and from the conference, which is great. Part of my itinerary involves visiting a good science friend and her fiance, whom I've not had the pleasure yet of meeting. So I'm looking forward to that. In other transportation news, I have a bike now that I can use, so I'm less limited to finding rides from other people, although I did manage to secure a ride to the airport when I get back next week, so that I can pick up the lovely miss Bait when she comes to visit :-D

The only other positive bit of news is that I sent out a letter of interest and my CV this morning to a post-doc working on a field project in the southeast who's looking for field technicians for the fall. They do neat work, looks like it could be a fun job. Got a response back pretty quickly, and it looks like we could be meeting up next week at the conference to talk in person. So in a few days I might know what I'm doing this fall! This would excite me, as I'm getting a little tired of the place I'm at now, and having a cut-off date would be nice, especially if it gives me enough time to visit friends in relatives on my way back home, as well as spending some time back at my old college with Bait and some old friends. I'll keep y'all posted on what I find out.

I have a feeling this has been a pretty long post, so I think I'll end here. Want to get some good sleep tonight, as tomorrow I have to pack up my belongings again, and figure out what I'm going to stash here for my return, and what I need to take with me for my travels. I'm going to try to pack really light so that I can be really flexible in the coming week; we'll see.

Take it easy out there everyone!