Wednesday, December 22, 2010


At this point, 3 of the 4 people I want as committee members are on board, but I'm still waiting for a response from #4. Sent an email on Friday (as I was advised that this can be a nice way of asking as it doesn't put profs on the spot), and had no response by mid-day today... Sent a super-polite reminder email to make sure email #1 hadn't gotten lost in this person's inbox. Still no word. It'd be so nice to put this to rest before I leave for Christmas! Oh well; I have a back-up plan just in case (but it would make my life more complicated, by potentially adding a committee member from a different institution/state).

All kinds of planning going on right now too, for traveling to a conference (in a warm place!) coming up in Feb, plus applying for a fellowship to spend some time in Scandinavia next year (where my advisors will be during a sabbatical). Busy busy busy!

R function currently blowing my mind: melt() and cast() in the reshape library (the built in use of aggregate is fabulous).

Thursday, December 16, 2010

Taking another step (committee!)

Lots going on in real life that I'm not going to write about now (what else is new).

Big news for the moment is that after months of procrastinating/agonizing, I finally just sent an email to a former professor asking them to be the first member of my graduate committee. This is a big step for me; I've been writing and re-writing the email all week. I really really really hope that this person answers with a big YES, because I think that their knowledge and experience would be invaluable to me, and in a number of ways their work is closer to what I want to do than my own advisor's. In general, I'm still skeptical of the value of committees, but I can totally see how this person would fit in. Part of my anxiety about it is that if the answer is no, I can't think of anyone else even at this huge institution who would be able to fill a comparable role. Mostly I'm filling my committee because the rules say I have to, but I'd really love to work with this person more.

Anyways, that's where I'm at. Cross your fingers for me.

With the holidays coming up, maybe I'll post more, including the list of favorite R functions I've been accumulating.

Theo out.

UPDATE: Success!! Big weight off my shoulders. Now I can ask other people on my list.

Tuesday, October 5, 2010

In search of great ideas

Not surprisingly, I'm still on the hunt for a great thesis topic. My advisor and I have been meeting weekly, and while he says that I've got a couple of established projects that could become solid PhD theses, it's early enough yet in my graduate experience that I can still spend time challenging myself in search of a super-shiny topic. So we've been putting a good bit of thought into what makes particular topics time appropriate, influential, etc, such that they result in classic, highly cited papers. Good things to think about, but not always entirely obvious.

The last week or so was dubbed ' 70's week ', and we've been hitting up a bunch of classic papers from the 70's. Some of them are terrible, some of them are pretty neat. Mostly what I've been struck by however, is the realization that a lot of the topics that turn up in weekly lab meetings and paper discussions and over lunch at the cafeteria - they're not really 'new' hot topics to the extent that I usually consider them. I've been surprised by just how much these 'old' papers are really discussing the same ideas that we still wrestle with today in ecology and evolution. Sure their discussions tend to be a little more qualitative and verbal than quantitative, and they aren't using all of the powerful new methods and resources that have been developed more recently. But a lot of the ideas are there.

Maybe I shouldn't be so surprised - lots of smart people have been (and are) ecologists. Wading into the literature though has been a good experience. I am both comforted and somewhat stymied by these realizations though - on the one hand, it's good to realize that even though a lot of the really foundational ideas in our discipline have been thought out and written about for decades, people are still making a living and doing good work to flesh out these ideas without having to come up with paradigm shaking new concepts. On the other hand, while I'm challenging myself to try to come up with a super shiny new idea, it's intimidating to realize how much has already been though out/discovered, and the extent to which most of what is done these days is 'just' filling in the blanks.

Ok, back to the late 70's....

Monday, September 27, 2010

Where do classics come from?

Quotes from R. McIntosh, "Citation Classics of Ecology"

"A less professional recognition was given to a Scottish landlady who fed J. H. Connell very economically, and stretched out his G. I. Bill funds. [...] Collateral stimuli were attributed by some authors to liquid refreshments ranging from soup to bitters and to the cup that cheers without inebriating, tea."

"Several [Ecological Classics] were explicitly considerations or tests of theory, and some urged the utility of theory as a guide in their research. Paul Dayton, however, among others, had reservations. He commented, 'Ecology often seems dominated by theoretical bandwagons driven by charismatic mathematicians; lost to many is the realization that good ecology rests on a foundation of solid natural history...'"

Sunday, September 19, 2010

Grad students are people...

"Initial premise: Graduate Students are People.

Graduate students can be described by models identifying their many functional and structural roles in research labs, field projects, classrooms, and budgets. However, the most encompassing model of the nature of a graduate student is the humanistic model, encompassing submodels of both physical and psychological well-being. Given this premise, a long list of corollaries can be developed. [...] "

- D. Binkley, 1988. Some advice for graduate advisors. Bulletin of the Ecological Society of America, 69 (1): 10-13.

Tuesday, August 24, 2010


"A wonderful fact to reflect upon, that every human creature is constituted to be that profound secret and mystery to every other. A solemn consideration, when I enter a great city by night, that every one of those darkly clustered houses encloses its own secret; that every room in every one of them encloses its own secret; that every breathing heart in the hundreds of thousands of breasts there, is, in some of its imaginings, a secret to the heart nearest it! Something of the awfulness, even of Death itself, is referable to this. No more can I turn the leaves of this dear book that I loved, and vainly hope in time to read it all. No more can I look into the depths of this unfathomable water, wherein, as momentary lights glance into it, I have had glimpses of buried treasure and other things submerged. It was appointed that the book should shut with a spring, for ever and for ever, when I had read but a page. It was appointed that the water should be locked in an eternal frost when the light was playing on its surface, and I stood in ignorance on the shore. My friend is dead, my neighbour is dead, my love, the darling of my soul, is dead; it is the inexorable consolidation and perpetuation of the secret that was always that individuality, and which I shall carry in mind to my life's end. In any of the burial-places of this city through which I pass, is there a sleeper more inscrutable than its busy inhabitants are, in their innermost personality, to me, or than I am to them?"

- Charles Dickens, "A Tale of Two Cities"

Wednesday, August 11, 2010

Changing structure of scientific inquiry

At ESA the other week (this post got slowed down by my now traditional post ESA cold), I attended an intriguing symposium on Ecoinformatics that led my thoughts in an interesting direction. Ecoinformatics (short for Ecological informatics) is, broadly, concerned with solving the technological challenges of making the increasing wealth of ecological data broadly available, accessible, and analyzable (?). In the symposium, several presentations were given on different efforts to unite existing ecological databases (DataONE) and to create a system for authors to submit datasets related to their publications (Dryad - which currently focuses on evolutionary biology, not ecology specifically).

This second project I find particularly exciting. There are many challenges that need to be worked out to make it a reality, but I really just want to comment on a few of the things that I found especially cool:

1) Authors will be expected to submit properly formatted and annotated data related to their papers for archival at the time they submit papers for publication. If done well, with an appropriate system, this means lots of cool data available to the scientific community allowing many interesting synthesis and modeling projects, and potentially fostering many cool collaborations. (Obviously lots of interesting challenges involving appropriate citations, etc, embargoing sensitive data or allowing authors more time to publish follow up papers, infrastructure issues, funding, etc.)

2) I was amused thinking about how this would mark a further step in the Ford-ification of Science; already within big lab groups, PI's have Big Ideas and write grants and get funding that supports various post docs and grad students and technicians who experiment, collect data, and analyze it. Open access data sets could compartmentalize science even more, making it totally possible to do great science and synthesis without ever collecting data. Fascinating to think about. Specialization can bring rewards in terms of skill levels at particular tasks, and increased efficiency, along with new challenges, such as making sure that appropriate data are gathered, and that communication between roles is good.

Anyways; fun to think about.

Sunday, August 8, 2010

Back from ESA

Just returned from an intense week of ecology thanks to the ESA's annual conference in Pittsburgh. It was a stimulating and eventful meeting for me, and has me motivated to start blogging again occasionally. As soon as I unpack, do laundry, water my plants, attempt to rescue my garden besieged with weeds, make dinner.........

Tuesday, March 9, 2010

Day 3 update: the magical land of spring-break campus

Ok, so today went a little differently than expected...

I read in the morning as usual for this week, but did so at a coffee shop in near campus instead of at home, to mix things up and to get some caffeine into the system. Spring break is a marvelous thing - I didn't have to wait in line at the shop, I didn't have to fight for a table, and I didn't have to wear headphones to drown out the usual crowd of students and others. I got a seat near the fire place AND the window. Magical. Walking around campus is a lot more fun too - fewer cars, fewer maniacal bikers trying to run me over, and fewer slow walkers to dodge (yeah, I'm one of those fast-walking types). The only downside is that the library closes early. Ooops. Guess I'll have to wait another day before delving into the catacombs of hierarchy theory.

Mid-day I showed up at one of my reading groups (having not been prepared enough last week to imply upcoming absence). But it was cool - one of the better little interactions I've had with such groups - everyone was tasked with bringing a single slide containing graphs/analysis of data they've been working on. I think I was the only one that rigidly followed the directions, managing to get 5 graphs intelligibly on a powerpoint slide. It was cool though to hear really succinct tidbits about a real diversity of different projects in progress - I feel like I learned something interesting from each one, which is more than I usually expect.

However, the downside to all of this is that, in addition to taking me away from my reclusive reading for a while, it also got me thinking about my current data analysis project again... and I had new ideas that I couldn't wait to try out. It's possible that I spent pretty much all afternoon tinkering with R code. But my new stuff works decently well (still a bit kloodgy) and I think it will save me a lot of time in the coming weeks, as I've been able to generalize a function so that I can give it in short notation the statistical model that I want to fit, and it will go off and do it for me, without my having to write out explicitly what I want each time with minor variations and new names. Pretty exciting. Now if only I could do it more elegantly.... hmmmm

BEWARE: Caution my dear readers; for those of you not already hooked... programming can get really really addictive. It has a way of inspiring the feeling that the breakthrough you've been waiting for is just around the corner, and then holding out success on you for hours or days on end. In this case, I've got a general formula now that lets me combine multiple linear regression and multiple logistic regression on two different distributions combined in a mixture distribution and fit in one fell swoop by maximum likelihood analysis. Fear me.

Oh, and it makes pretty graphs too.

Tomorrow I will strengthen my resolve and return to another day of reading. It's supposed to be rainy too, so I'll be less inclined to frolic around campus pretending that I don't have to share it with anyone. I'm off to delete a few dozen emails before bed.

Theo out.

Monday, March 8, 2010

Think Week: Day 2

Ok, time for an update on think week - this'll help make me draw my thoughts together. Just got back from a lovely sunny walk to a park down the street... it was nice enough that I wore my spring jacket and sat on a bench in the sun writing for a while! Spring here we come!

At this point I've polished off pretty much all of the articles on the reading list I put up yesterday. Some I read with greater attention than others; several of them are reviews of books that I'm going to get out of the library when it's open again. Together though, they cover about 2 decades of an on-going discussion about whether or not general ecological laws can exist, and if they can what are they, do they matter, and have we found them yet? Lots of comparisons an analogies are made to physics and other disciplines (these are part of the 'physics envy' debate). I think collectively, too, they're part of a (relatively) young field attempting to define and justify itself, something that at least traditional physics has moved beyond long since. Some of these papers were suggested to me during a discussion I had with an empiricist about what theoretical ecology is as a field/discipline (a definition I'm still turning over in my head).

In an attempt to summarize:

Ecology is a complex field. Complexity varies with scale relative to the observer, and just how complex something is relative to our attempts to predict it depends on the number of interacting entities involved, the nonlinearity of their interactions, and the degree of precision desired in predictions relative to the scale of the interacting entities. By way of analogy to physics (as is so often done) - when we deal with systems of many interacting particles, like gases, we can predict their macroscopic properties really well, drawing statistical conclusions and looking at average behaviors. But any physicist would be pretty unhappy about having to predict the exact trajectory of an individual gas molecule, or even a collection of them.

In the same way, as Lawton and others point out, within ecosystems the number of interactions that occur between different species and their environments is large. Broad scale patterns as explained by a growing number of macroecological ideas are somewhat easy to capture, arising out of statistical relationships and generalizations (ie, we can predict general relationships between species abundances and distributions, body size and geographic range, etc). On the other hand, he points out that we're also increasingly good at working with population level dynamics, and developing general principles governing them, like physicists can predict the interactions of a few particles. But we get stuck at the intermediate scale of communities, which are a whole bunch of species interacting locally. A lot of this makes sense and rings true, although I think the outlook for community ecology is a little brighter than he made it seem; we are tracking down relevant mechanisms, and weaving them together and understanding more all the time.

The crux of the matter though, is that making good predictions at the community level is really important, because in many cases, that's where a lot of our visible ecological/environmental problems are taking place. That's the scale that managers work at, and the level at which endangered species are handled often. So some of the greatest need for strong predictions arise at scales that may be fundamentally the hardest to understand and generate predictions for, without the time and resources to do a lot of comprehensive and often case specific studies. Also, a lot of what we find most compelling about ecology are all of the fascinating stories of unbelievable species interactions, incredible organisms and wacky environments. Good thing I like a challenge.

Seems like there's a tricky balance between 1) throwing up your hands despairingly and saying we can never know anything general about communities and will have to studying all of them individually, and 2) looking too hard for a holy grail of generality that may not be feasible. You don't want to get so focused on a particular species or system that you lose all perspective. And at the same time, the only way we're going to get anywhere is by looking at a bunch of deep case studies of communities in particular systems and searching for patterns and interacting mechanisms. How does all of this fit in with the scope and time scale of a PhD thesis? Holy grails take too long and are risky, and organismal myopia is bad for job prospects down the road... I need to figure out how to trace a middle road.

Topical list for tomorrow (Time to start getting more concrete):

- whole lake manipulates by Steve Carpenter et al.
- check out papers, yet to be selected, on microcommunities in pitcher plants and bromeliads
- finish a great conceptual paper on spatial coexistence, drawing together a body of theory (Amarasekare. Competitive coexistence in spatially structured environments: a synthesis. Ecol Letters (2003) vol. 6 (12) pp. 1109-1122 doi: 10.1046/j.1461-0248.2003.00530.x)
- check out this crazy topic I stumbled on earlier, "Hierarchy theory"
- a few papers from the voluminous works of Bob Holt
- having finished off the ~17 papers in my big ideas folder, it's time to take a whack at the 52 in the regular to-read pile.

Stay tuned for more!

Two of the more formative papers from today's reading:

Lawton. Are there general laws in ecology?. Oikos (1999) pp. 177-192
Simberloff. Community ecology: is it time to move on?. Am Nat (2004) vol. 163 (6) pp. 787-799

Sunday, March 7, 2010

Spring Break = Think Week?

Apparently Bill Gates has a long running tradition of holding 'Think Weeks', where he would retreat to a small, remote cottage and spend a week intensively reading papers (to the tune of more than a hundred a week), thinking about up and coming trends in the technology business and how to strategically direct Microsoft over the coming year and beyond. Also drinking lots of orange soda. Check it out here.

I mention this because I've been planning my own variation on 'Think Week' this coming week, coincident with our spring break and a brief respite from coursework. Goals for the upcoming week:

- Try to read everything in my 'To Read' category in Papers (currently sitting at ~52 papers)
- Follow my nose beyond that
- I'm going to start really broad, with a set of commentaries on ecology, theoretical ecology, and where they're heading (the good, bad and ugly), then towards the end of the week start to read more narrowly

Best case scenario, I'd like to emerge from the end of the week having identified:

- 1-3 topical areas that I would enjoy doing a dissertation on,
- 2-3 theories/models related to these topical areas that I could try to test with experiments (and possibly additional theory) over the summer.

This blog is going to be one of the outlets for me to keep myself on task, as well as collect and summarize my ideas a bit. I'll try to post a daily reading list of what I've been looking through each day. Suggestions of other good articles are most welcome.

Here's my queue for today (Big ideas in ecology):

Monday, March 1, 2010

Stumbled upon: "Humpty Dumpty Effect"

Whilst reading a review (Young et al. 2005, Ecology Letters) in preparation for a reading group I might sit in on, I stumbled across the term 'Humpty Dumpty effect'. After a good chuckle, I did a bit more side-track reading to find out about this curious monicker. Check it out, it's pretty cool:

In other brief news, I finished my review of that manuscript and turned it in; we'll see where it goes! It was an interesting learning experience, and I think (hope?) I did a pretty thorough job. I've also kicked out two abstracts for conference presentations; Transient Theorist is going to be at MEEC and ESA this year! (Pending ESA's acceptance, technically). Now I just need to figure out where I want to head with research this summer...

More posts to come towards the end of the week; I've been squeezing in some interesting reading on general theories of ecology, and other articles trying to define what our field is, what it seeks to do, where it's heading and if it will ever get there. Heady stuff. Not sure what I'll have to add to it, but it is really interesting to think about - I should practice defining and justifying my discipline more concretely and more often.

Friday, February 19, 2010

Not again...

It is really discomforting to have your grad advisor tell you that probably you should have chosen a different program/institution, even when it's said with the best of intentions in a friendly manner and a "hindsight is golden" attitude. This is the second time I've heard this from him. It doesn't make a bit of difference now where I could have gone, this is where I am. All that is accomplished by saying that is adding another little dent to my self confidence, which is a little shaky right now as I still have no concrete plans for the summer or a dissertation topic. It's challenging enough for me to stomp out the little voice in my head that says the same thing, without it being aided by external confirmation. Oh well. I'm sure it's not intentional; certainly not his fault that I'm feeling fragile.

In other news, I think I've just about finished writing up this manuscript review. I think it's a little long and I probably have spent too much time on it. Not going to submit it right away, as I want to take another look at what I wrote again tomorrow. I want to make sure I'm not either making what I wrote too harsh or too accommodating due to today's fluctuation in my confidence/anxiety levels. I've got another week anyways; maybe someone will look over it too. Wheeeee!

Tuesday, February 16, 2010

Scientific writing + Plagiarism in different disciplines

So I read through the manuscript that I was asked to review, and I've decided to go for it. It's not directly in an area with which I have tons of experience, but I know enough about it in a general way that I've been able to do some background reading and browsing through the references to get up to speed. If this were a longer paper, one with more technical difficulty, or for a higher level journal, I'd ask for a rain check. But I've decided that I can do this, and it will be a learning experience, and I have to start somewhere. I'm up to the challenge. And hopefully I'll be able to get a reality check/advice from either my advisor or a good friend and post-doc in our lab.

I'm only about halfway through an intensive reading of the manuscript, and it's already raised some interesting challenges and presented me with issues I've never thought about before. I'm feeling more and more like I'll actually have some useful advice and critiques to share. I have suggestions already for improving the intro, extending and clarifying the analysis, and even on a technical aspect of a certain statistical test/related assumptions.

One aspect though is particularly tricky; to summarize (while maintaining confidentiality)...

My big question for this post is: What constitutes plagiarism in scientific literature? (I've heard more than one person refer to the Supreme Court quote "I know it when I see it" during discussions of this topic). I have some previous experience working as a peer tutor for college level english courses. As you might expect, as a discipline, English/Literature seems to me to place much more emphasis on particular sequences of words or phrasings as being the intellectual property of an author. To avoid plagiarism we advised students to substantially paraphrase and reword similar sentences, or to use a cited, direct quote employing lovely punctuation: the ever popular " and ". In this paper I'm reviewing, after looking up references, it has become apparent to me that entire sentences can be traced to previous articles by different authors, almost verbatim (usually with the omissions or substitutions of only a couple of words).

Now I'm left to wonder how big of a deal this is. It makes me uncomfortable because I know it would be a problem for the english students I used to advise, but this is a different context. Scientific writing is necessarily more precise, and often there are fewer alternative ways of saying the same thing. The emphasis in science is on the creativity of research ideas and methods, the ideological content that is conveyed by language, and less so on the creativity of language used for communication.

Further muddying the waters, after looking at several of the citations, its clear that existing papers in the literature also use very very similar language when describing this particular kind of model, although usually these are multiple papers by the same author (not the same group as the one behind the paper I'm currently reviewing, and in better journals by and large). Is it ok to plagiarize yourself? If other papers in the literature use such identifiably similar language, is this standard for the discipline and I just haven't paid close enough attention before?

I think that a really important aspect of plagiarism is intent. Intentional and willful plagiarism without appropriate citations is a much more clear cut situation in my opinion - it's flat out wrong and demands serious consequences. Unintentional plagiarism is more grey, and I think requires more subtlety in its resolution. In this particular case, it's likely that the authors don't speak English as a first language, and there's no obvious intent to disguise the source of the models and ideas as citations are given. If direct quotes and quotation marks were used, I wouldn't blink (except for how rarely direct quotes seem to show up in journal articles). The wording is just soooo similar. Some journals have (relatively) clear policies on this, but not the one I'm reviewing for.

I'd love to hear what you all think... Are standards for plagiarism different in different disciplines? Should they be? And, (this is the part I'm stuck on right now), what is the appropriate role of a reviewer in this kind of situation? What kind of accommodations, if any, should be made due to linguistic and cultural differences in the peer review and publication process, especially as research becomes more and more international?

In upcoming posts I'll say more about this process as I work through it and figure out more about the role of a reviewer.

Theo out.

Friday, February 12, 2010

The hazards of being a scientist

As a graduate student, I do a lot of writing. And when I do mathematics, I really like begin able to write in multiple colors; it helps me see different parts of equations, or pick out particular variables, or make clear thought-graphs. My favorite pens for the last several years have been this kind:

I can get them in packs of 5 or 6 different colors, they're great. Lots of ink, they last a long long time. (Tiny caveat/caution - I no longer take these with me on plane trips to conferences, etc, as the change in air pressure seems to cause them to leak more often than not).

However, as I learned the other day, it's a very bad idea to say, absent mindedly place one of the red pens in your pocket without putting the cap on it first. About halfway through the day I noticed a huge red splotch on the side of my pants. (Not being cool enough/well dressed enough to wear a shirt with pockets on a regular basis, and not having found a pocket protector made for pants, I often carry my pens unprotected in my pants pocket). About half a reservoir's worth of red ink had soaked into my jeans. A stack of paper towels later, I was able to absorb enough of it to not risk staining anything else. But I had to spend the rest of the day walking around looking like my leg was gravely wounded.

The side of my leg is still pink, although I've had some success getting the stain out of my pants surprisingly. I let them soak overnight after rubbing in a baking soda paste, and then washed them with some oxyclean. The next time around, I figured that if baking soda paste worked well, then things could only improve if I rubbed in some baking soda paste and then dumped some vinegar on the stain. I mean, who knows, right? That was always the best course of action back when I was a practicing kitchen scientist. And I have vague notions that maybe the CO2 production will bubble through the fabric and release the ink somehow. Probably crazy... but it sure was fun to mix the two together again!

So, the moral(s) of this story:

1) Always use protection.
2) When in doubt, use vinegar and baking soda.
3) Maybe remember to put pen caps on before jamming pens into your pocket.

Theo out.

Science + Romance + NPR

Does it get any better than that combo?

Check out their neat story about the Voyager project that brought together Carl Sagan and Ann Druyan here

Wow. And you can listen to parts of the recording of language, music and biology placed on a gold record and carried onboard the Voyager spacecraft as they push on into outer space.

Monday, February 8, 2010

Writing a review???

The other day, I opened up my email, and found a message from an editor at a lower-level, peer reviewed ecology journal. This polite message was address to "Dr. Theo Miss-spelledLastName", and turned out to be a request that I consider reviewing the attached manuscript to evaluate it for publication in their journal, based on provided criteria.

First reaction (worth enjoying):
WOW! This is pretty exciting, I've never gotten such a request before. And it definitely counts as being another little step towards becoming a bonafide scientist.

Further reflection:
Peer review is a hugely important part of scientific pursuits; it's what helps us set and assure standards of quality, rigor and academic integrity in our discipline, both in the work of others, and in our own. Reviewers to the best of my knowledge usually remain anonymous, so they are free to provide honest, critical (and hopefully constructive!) opinions without fear of political/career repercussions. In its most idealistic sense, it also helps to free the evaluation of the merit and originality of ideas from being dictated by a limited number of people (publishers, editors), making science more democratic, and hopefully dissuading the rejection of an idea because it is unpopular, instead of actually unsound. (Whether or not this always works out the way it should is certainly a matter of some debate).

Any paper submitted to a journal that goes out for review usually needs at least two reviewers. Without doing any explicit math here, I'm sure you can see that the number of reviewers needed to evaluate all of the papers being submitted to this, and other journals, adds up pretty quickly! Most of this process is handled through a sort of unspoken karmic system - one of our responsibilities as academics that want to have our own papers published someday is to also serve as a reviewer for the work of others. When people do their share, this helps support the important goal of maintaining an effective peer review system. (This is overly rosy and deserves qualifiers; I know that less than ideal things happen, but I don't want to go into that at present).

I'm a little conflicted over this one. I'm excited and honored to be asked (although I'm sure in a few years it'll seem like no big deal), especially as someone must have referred me - which probably means they think I can do a good job. I want to do my karmic share. Then, on the other hand, I'm no expert, I haven't even published yet myself (just one failed attempt), I have a lot yet to learn and a bunch of projects on my plate, and they didn't even get my name right.

Another part of the karmic system is that the not-yet-published manuscripts that you read as a reviewer are held in confidence - in other words, you can't take their ideas before they've published them, or copy their work, or distribute it to other people. I don't know if this is kosher or not, but I did take a brief look through the paper to try to get a sense of how challenging it is prior to making my decision... I think I could do it, although certainly not as well or as thoroughly as someone with more experience and knowledge.

I'm going to sleep on it (again), and will make a decision tomorrow; I don't want to slow down the process if I choose not to review it, as they'll have to locate someone else. Otherwise, I have several weeks. I want to do my share in order to do right by the system, but I also want to do right for the authors of the manuscript and make sure they get a fair, knowledgeable and useful review.

Wednesday, February 3, 2010

Ups and downs

So lately I've been feeling very positive about my work and productivity. To summarize:

- I'm keeping up with course work for two classes
- I've presented at two different lab meetings
- I've attended a slew of seminars
- I'm making significant progress on two different manuscripts both headed towards publication, on both of which I'll likely be first author. Not earth shattering work, but interesting and solid in my opinion.
- I'm learning LaTeX
- I've been able to squeeze in select reading on a potential study system, and I'm feeding myself small morsels of a plant ecology text book and absorbing more knowledge on hierarchical modeling.

So I'm doing all of this stuff, and making lists and evaluating myself and checking things off. Which is good. Feels way better than last semester, and I'm more involved and interested in what I'm doing.

But somehow, all it took was a 30 minute interaction with my advisor while walking across campus, containing the phrase 'So, do you have any more thoughts on your thesis and what you want to do this summer?' and now I feel like everything that I've been doing is just filler, because I don't feel a bit closer to figuring that out or converging even slightly on a topic. 0 to substantial anxiety in under 60 seconds... yeehaww. Major downer.

I'm enjoying a lot of what I've been up to, even writing (!) which I often find to be a struggle/boring. But the more I think about it, the more I'm convinced that I'm far too tool oriented. I like problems where I learn more tools - different programming languages, different mathematical techniques, more statistics or experimental methods. I'm fascinated by all of this technology... But I think I have to stop picking out projects based on the tools I get to learn! I really should be selecting them based more on the questions they're addressing... otherwise I'm going to end up being a hell of a technician, but probably not much of a scientist.

The sensations are very similar to my experience last year trying to pick out a graduate school/advisor, except there the alternatives were well defined and finite. This decision could be just as significant/important, but is so much more open ended. There's no way to make up a pros and cons list of insanity like I did last year. I don't know how to tackle all of this, particularly when it's so easy to fill up all of my time working on other things. Ugh.

Tuesday, January 19, 2010

Intimidating questions

For one of my seminar classes this semester, I'm supposed to answer the questions:

1) If you were to write a single paper on your dissertation research, what would be the title?
2) What is the most important unresolved question in your field of research?

Panic mode! These are very important and cutting questions, that I need to think about... but which I feel vastly unprepared to answer. Given that I have no dissertation research yet, or even a dissertation topic. And given that I'm still learning more every day about my (broad) field of research. I've been procrastinating, but I only have an hour left so I'm about out of time.

I wrote down a bunch of keywords for the things I'm interested in, and did a google search. Just to see if any insane people have tried combining ALL of these topics at once with any success. Surprisingly, a paper by my advisor came up as the fourth hit. I guess that's a good sign, as I sometimes wonder if I'm in the right lab (probably not a unique worry).

Ok, time to hammer out some BS title using some of these words and picking a system.

Thursday, January 7, 2010

2010: Graduate Semester Two

*high five* if you get the subject line book reference...

One of my biggest "New Years" resolutions this year has got to be trying to implement regular, constructive evaluation of my work and progress. I need the self-awareness and motivation that I hope this will increase. In this spirit, I tried to put together a big big list of what my goals are for 2010, academically and personally. Things I would like to do. Things that I have to do, but hope to do well. Almost all of that list is here (it's long, no obligations to read it):

  1. Dissertation topic - I need one. Even in a vague incarnation. So that I can start directing my reading, and planning summer experiments.
  2. Graduate committee - this sort of has to happen after #1, but also has to happen before I know that I've finished my coursework.
  3. Publications - I'm currently sitting on 2-3 projects that, if written up appropriately, could almost certainly be published somewhere. I need to do this. I've been sucking at making headway, mostly due to procrastination, and this needs to change if I'm going to make this science thing work. I care less right now about where they get published than that they do get published somewhere, and that in the process I start figuring out a good system for writing. Maybe I need to schedule a weekly time for doing this.
  4. Finish coursework - after this fall's experience with classes, I've pretty much decided that there aren't anymore classes that are really important/useful for me to take, that I can't learn more efficiently and effectively on my own, if I'm disciplined enough. I wasted a lot of time. Now I want to finish off the bare bones requirements that I have remaining, and move on (there's some hope of actually accomplishing this by the end of this semester, subject to the dictates of the committee I need to assemble - see #2).
  5. Be selective about seminar attendance.
  6. Take better notes - when reading and in seminars. Things make sense at the time, but I don't remember them as well as I usually think I will. I also need to take notes in a more organized fashion so that I actually can find, and go back and look at the information I bothered to record.
  7. I need to start practicing generating ideas. I'm going to get a special notebook and write down all of my crazy ideas and questions. Maybe I'll keep track of how many I have each week.
  8. READ MORE - fewer classes for me this semester. I need to sit down and actually read through the stack of interesting books and reference materials I have fun picking out but rarely actually read. Same goes for journal articles. I'm good and finding and collecting them, I need to get better at internalizing them.
  9. Statistics - one of my old undergraduate bad habits reappeared this past fall. Despite loving my statistics course, I shirked on the reading from the assigned texts. I really need to go through this stuff, I know I would find it interesting and useful.
  10. Learn LaTeX - I'm auditing a seminar on this weekly.
  11. Spend less effort on classes and more on my own scientific interests - probably.
  12. Remember to be EXCITED about what I'm doing and the opportunities I have.
  13. Every time I read a theory paper, I need to try to think up a corresponding experiment. I've decided there's no one around here that's going to force me to think about this - I have to push myself to do it if it's going to happen. And this is a skill I dearly want to have, so I don't end up spending my life generating, but never empirically testing, theories.
  14. Table of Contents - I signed up to receive a lot of them. So I need to actually read them instead of letting them sit in my inbox for a few weeks and then deleting the backlogs.
  15. Learn about experimental opportunities at my field station - talk to people about what they're doing, and what resources, data sets and opportunities are available to me as I'm designing my own project.
  16. Hang out with more empiricists - I'm going to try to sit in on some lab meetings of another lab group that does a lot of good empirical work, again as part of trying to train my brain.
  17. Reading lists - I want to find a good way to compile them and actually make use of them, instead of just dumping reading material into folders from whence it rarely again sees the light of my LCD screen.
  18. Self evaluation - On a regular basis, look at my goals and evaluate my progress towards them.


  1. Regular exercise - this makes me better mentally and physically. I need to set up something regular here in the city; attending weekly soccer games on friday nights out at the Bio station didn't work well - by that time I was always just too tired mentally and physically to have the motivation to make it happen. I may join a different team here in the city; my cousin and I are also going to try to set regular racquetball matches.
  2. Break some habits - less TV, less eating out, a few other things
  3. Food - do a better job of eating regularly, more fruit, less processed stuff. I should do this to unwind instead of TV shows on hulu.
  4. Plan my garden - for this summer out at the station!!! very exciting
  5. Spend less time being stimulated - that probably sounds weird. What I mean is, not spending 12+ hours in front of a computer screen consuming random information and noise and visuals. I could use more regular, healthy doses of silence and existence, instead of information overload drowning out self reflection.
  6. Meet non-science people - I realized the other day that everyone I know here in the city, and actually the whole state, on anything like a friendship basis, is a scientist of one variety or another. While I love scientists, I really need more balance and diversity than this. Not sure how to go about it yet.
  7. Try attending the catholic graduate student group get-togethers - this might help with #5 and #6 if I stop chickening out.
  8. Sleep wake cycle - get up earlier, go to bed earlier, make both times more consistent. I'm a morning person, and I need to get that schedule back again, even though a lot of my friends are more night owls. I'll be happier and more productive.
  9. Correspondence - stay in touch with friends better.
  10. Say NO more often
  11. Do something creative and non-scientific
  12. Volunteer - I think I'd be happier if I were engaged in some fairly regular activity doing something with tangible, short term, realized positive results. Would make me feel less useless/pointless, and meet new people.
Might add more things as I think of them. This is a lot to do... but no one ever accused me of not being ambitious in my projects!!!

Happy New Years everyone!

Fall semester in review

The good, the bad, and the ugly (on fall semester academics):

  1. No one's kicked me out of graduate school yet, so I've still got them all fooled.
  2. I found myself more than capable of handling my coursework; frequently it felt downright easy.
  3. I had a great statistics class, learned some things, and did significant work on an interesting project.
  4. I've got a great labmate, and also a great cohort of first year students to muddle along with.
  5. Heard some really interesting and exciting talks given by various visiting seminar speakers
  6. Attended a neat, small conference and met some interesting people
  7. Gave my first lecture (~3 hours long, and technically at a graduate level!)

  1. I made no progress on writing up papers for either my undergraduate project (since August), or the project I completed prior to graduate school as a technician working with my advisor (and presented on at ESA in August). This is kind of inexcusable, since both of them are pretty much sitting around, results in hand, and crying out to be written up and published.
  2. My courses frequently felt too easy. My typical response to this is to get frustrated with the subject, unmotivated and rather apathetic. This didn't matter when the course in question was "Technical Theater" or some other course for my liberal arts undergrad degree. This matters a lot, and is harmful, when the course in question is directly related to my field of study for my graduate work. I spent a lot of time feeling frustrated that classes were too easy and I knew too much for them, and simultaneously feeling extremely overwhelmed about how much I don't know about my field, etc. Again, this didn't help much when it came to me getting stuff done. Something I need to rise above.
  3. Part way through the semester, I realized that I was attending far too many seminars because I felt obligated to do so, rather than because their content matter was interesting to me (there are a lot of seminars that happen at a university this big). Then, as a result, about halfway through the seminar my attention would wander, however caffienated I was, and I'd spend the next 30+ minutes with open, glazed over eyes, staring into space in the general direction of the speaker. In at least one instance, this unproductive stupor carried over into the rest of the afternoon following the seminar, and in my attempt to get home I took the wrong bus twice before it all wore off.
  4. Not enough critical (= useful) self evaluation and too much self criticism. I just sort of worked at whatever was on the top of my vaguely defined to-do pile, hoping stuff would get done, and drifting along, with the tensions mentioned above. I need to intentionally and constructively review my work and my progress towards defined goals on a regular basis and try to discipline myself more. If I can make myself do it, this will be much more useful and productive than maintaining a constant, diffuse, critical feeling of being inadequate.
  1. Deciding that because my classes felt too easy all semester long, I'd pick out very very challenging topics/projects/analyses for my various final projects and finally challenge myself. Challenging yourself is good. Challenging yourself on 3 different fronts simultaneously under a 2 week deadline is ugly.
  2. As my (more assertive) lab mate has observed and pointed out to me, I don't tell people 'no' often enough. I like being helpful, and am very loyal to my friends, but I need to set boundaries for myself so that I don't let these traits, and the interactions that result from them, consume all of my time and energy. I'm sure this is something I will face in the future when (if??? long story) I get a TA position, but there the official nature of my position will help me draw a line. With friends, fellow students, etc, it's a lot harder for me to say no. As I have fewer classes this semester, it'll help, as there will be fewer classmates asking for help. It's not my job to teach them - that's the professor's job (at one point this semester, the prof for one of my classes was very busy, and referred a few students to me to get questions answered. This is ok when I am established and know what I'm doing, but this past semester it became a significant time sink when I really need to be getting my own act together). I also need to place some restrictions on what sorts of collaborations I engage in. I have some ideas on this, but it's a topic for another post.

Fall semester was far from a disaster, there are a lot of good things going here, and I learned some stuff. I didn't accomplish a lot of what I wanted to, but I have some ideas why, and on how to do better this Spring. I've got some good friends, have handled living in a city and being more independent than ever. I haven't been kicked out, and I haven't lost my enthusiasm for the things I do.

Next blog post: Goals for 2010/New Year's resolutions.