An e-mail I hope to get more often

In the midst of trying to write a manuscript, dealing with data glitches, and putting together the first edition of The Accretionary Wedge, I received an e-mail from the chair for a session at the upcoming American Geophysical Union (AGU) annual meeting in December.

I sent him a note, asking about the session, whether it was an oral or poster session, and so on.
And then I get this note back:

I have added you as an invited author.
Cheers,

Yay!
One less thing to worry about....although I do still have to actually submit something (deadline is Sept. 6th, by the way).

The joy of research

Not the e-mail I wanted to see from my collaborator this morning:

The calibrated ages for _____ show a major glitch re your attempts to
look at _____.

Awesome.

On the nonlinearity of drafting a manuscript

Do you write papers in a neat, orderly fashion? Kind of like they taught you back in grade school -- with the outline first, and then you go write each section and subsections?

I sure as hell don't.

I've been writing up another big chunk of my dissertation work lately (you'll notice my posting frequency has increased too....hmmm). I find it hard to stay in one section of the paper for more than 10-15 minutes. While working on the Introduction, I think of something I need to discuss in the....well, in the Discussion, so I type a few reminder phrases as a place marker. As I scroll back up to the Introduction I remember that I forgot to look up the number that goes where the highlighted red "X" is. That's right, I need to address that aspect in the Introduction so when I reveal my data later it all fits together nicely....yes, that'll be awesome! But, oh crap....now i'm opening a spreadsheet. Oh crap....I found a seemingly small, but cascading error in one of the tables. Did I really do that wrong? That was stupid. How bad is it?

Instead of dealing with it right away, I decide to go back to the text and finish my train of thought. What train of thought?


cartoon above from here

Submitting manuscripts online

So, I submitted a paper the other day, which was all accomplished with the internets. It was through the Manuscript Central web service, which i'm sure many of you have used. Their service hosts some 1,700 books and journals, which seems fairly ubiquitous.

Anyway...my overall experience was pretty good. Online submission has improved by leaps and bounds in just the last couple of years. This service is pretty slick....it integrates your main text document and all your figures and tables into a single PDF that is ready for download by your peers for review. It would be nice to have that capability when I'm preparing drafts of papers for co-authors and such. Obviously, it's not that difficult to prepare an integrated PDF these days, but still....to have one magical button that does it for you would provide more time for more important things.

But....I did have one problem. The figure upload feature tells you to paste your captions into a dialog box and they will automatically be associated with the figure and placed on a page preceding that figure in the final PDF. It didn't work. So, I had to be that guy who emails the editors and tell them something went wrong and my submission is incomplete. I hate being that guy.

The final stretch

The end of my PhD journey seems to be racing towards me rather quickly. I have a very loose, informal, "theoretical" defense date of December. My committee thinks this is reasonable but when I look at my calendar, I start to get a little nervous about it happening. What I learned from doing a master's, however, was that if you mark a date on a calendar months in advance the value comes in the motivation to make that date. Even if things get pushed back slightly, the idea is that if you hadn't marked that date in the first place, then you wouldn't have made as much progress. But....now that i'm already slightly waffling and rationalizing about making that date, can I say that the motivation is there? Ummm.....what?

Anyway, my particular program has, in the last 10 years or so, gone to a more "modular" dissertation. That is, instead of writing one, ridiculously long tome about a single project we have multiple projects that fit within a "theme", for lack of a better word. There are perhaps some disadvantages to the modular style that one could think of, but I think the advantages far outweigh them. Firstly, the separate projects or sub-projects are summarized in chapters that are meant to be stand-alone papers. This has been valuable to me because then the papers are already in a format suitable for a journal. Why write a 500 page monstrosity nobody is gonna read anyway and then have to transform it into a journal manuscript later?

If you read this blog semi-regularly, you can probably guess what my "theme" is. All of my chapters deal with deep-marine sedimentary sytsems in one form or another. Some aspects deal with fundamental processes more, whereas others are utilizing attributes of the system (distribution, composition, timing, etc.) to address geologic questions of the specific region.

I'm writing this post because the first major paper of this work is about to be submitted (finally). I remember saying I wanted to submit this back in April! The paper went a couple rounds with co-authors and advisor and is now ready. Today, I have to do some of the remaining annoying little tasks (e.g., tracking down the volume number for that one pesky reference). It feels good to have this chunk (nearly) done. In terms of finishing the PhD and getting through the defense, the more of my chapters that are already submitted to a peer-reviewed journal, the better. Having all of your work submitted by defense date is not necessarily required here, but things go much, much smoother if they are. Realistically, I'll have 2/3 of my work submitted by December with the remaining very close.

So, that calendar seems to be marked with bigger font and in bold now. It is no longer an "idea" or "something to shoot for", but is transforming into a real day. A day that will be here a lot closer than I think.

As for my post-PhD plans....I will post about that another time. Several months of individual soul-searching combined with discussions with my girlfriend about what she wants to do next, where would we want to live (or definitely not live), and so on. As you know, it gets compli-ma-cated. That deserves its own post.

Who said you could go on vacation...

...is what the grad-student-guilt angel is whispering in my ear on one shoulder. On the other shoulder is the holy-crap-you-deserve-a-break devil saying.....well, saying what he always says.

I'm gonna actually listen to the devil for once. I will be away from the internets (and phones even!) until July 2nd. In the meantime, check out some of the blogtastic goodies out there:

• Where on (Google)Earth? 2.0: Ron and the Lab Lemming are taking my WoGE series to new levels. Posts are now coming from and being solved by more people. It is getting a little more geological instead of pure trivia (which is great). And we have plans to make it even better as time goes on. Check out my geoblogosphere ticker on the sidebar for the latest....or check out their blogs directly (links above) for the latest. Click here to see all the old WoGE 1.0 posts.

• I've been checking out some new blogs of late as well (new blogs to me, that is).

• I'm not sure what The Anterior Commissure is, but it has something to do with neuroscience. This blog has some great writing about an area of science I have little knowledge about. The author, Kate, explains things with the right combination of technical details (to help further my knowledge) and the important why-should-we-care rationale.

• At first this blog led to decreased productivity because I spent time reading it. But now, the topics on Academic Productivity are helping me think about how to manage the information that I collect and compile.

• Letter Never Sent is a potpourri of interesting writing and ideas. I especially like the post about simplifying your life.

• Tamino has teamed up with Maribo and Eli Rabbett for a new series of climate science posts. These are not new blogs individually, but the collaboration, or 'mob blogging' as they call it, is a new approach. The posts at Open Mind continue to impress me with the caliber of analysis and explanation of a complex system like climate. Check out one of the first posts of this series over at Rabbett Run dealing with the fundamentals of the carbon cycle.

• I've also been enjoying the TED talks. Every year in Monterey, CA a gathering of very sharp people (scientists, technologists, economists, social activists, artists, etc.) present talks about their ideas. Now you can view or download these talks at the TED website. They have everything from talking about reverse engineering the brain to the promise and perils of nanotechnology to beat poetry. It is a very slick site in terms of choosing from the database of talks based on topic tags. And they've made it very easy to download right to your video iPod, if you happen to have one. Great stuff...check it out.

See you in a couple weeks!


image above from here

Metablogging

Why do bloggers eventually end up blogging about blogging at some point?

• profound realizations through examination and reflection of self
  
• running out of ideas
  
• too lazy to think of ideas
• something to do during bouts of writer's block while trying to write about about the controls on Holocene turbidite accumulation offshore of southern California

Regardless, metablogging can be an interesting exercise (am I meta-metablogging right now?).

Someone asked me the other day why I spend time with a blog. Good question. When I first started it (fall 2006), it was more of the public journal/diary type with some personal commentary. That was okay, but there's plenty of commentary out there...and some of it very well-written and engaging. I'm not one to share every thought in my head to the public at large so the diary type of blog wasn't really my thing either. As the geoblogosphere community grows, I find it more satisfying to post about earth science-related topics most of the time (although the beauty of the blog is to be able to throw in some random stuff from time to time....we all should take advantage of this wonderful self-publishing freedom). Besides, thinking and writing about geology is what I spend nearly all my time doing anyway.

Nowadays, I view this blog as the online equivalent of that person who, in the pre-internet days, would cut out and tack up various clippings from magazines or newspapers on their office door. I enjoy telling people about stuff I think is interesting but I really don't like bothering people. In that sense, the blog is perfect. Readers can check it out if they like...or they can move on. The majority of my posts are brief, contain a link or two, and include some imagery (photos or video) about a specific topic or current event.

I would love to create posts about the specific research i'm doing in a lot more detail. But, being relatively early in my research career, I don't have this stuff out in the literature yet. I'm focused on getting my work submitted and published in peer-reviewed journals first. When (not if) the papers start coming out, I will very much enjoy writing posts about my own research (i've got some stuff in the pipeline that will be featured on here soon). Others may disagree, but I think it's prudent to wait to put your science on a blog until it reaches a "cite-able" status. At least for work that one would want published. I think scientific blogs have the potential to be an appropriate venue for presenting original results someday too, especially review papers and others studies that look at previously published data with a new perspective or in light of other findings.

Managing information

What is the best method for organizing scientific papers and other references in the digital realm? This question is becoming increasingly more important for me in just the last year. The vast majority of the references I need are now available digitally (but I still do physically go to the library from time to time...which is a nice break from the office sometimes).

I have gotten so used to downloading PDFs, renaming them quickly with date/author/keyword, and then putting them in a subject folder. But I am getting so many now that I can't find them easily and I end up re-downloading the dang paper. This is not efficient.

GoogleDesktop search does a decent job, but I wish I could filter the search to one master directory so I don't get a bunch of unwanted search results. The problem is that one paper can fit into many categories (obviously), so I would like a fast and easy way to "tag" the PDFs with my own keywords.

Branner Blog has a nice post summarizing a handful of the bibliographic and citation tools out there on the internets. Check it out. I downloaded Zotero a couple weeks ago after reading a rave review of it, but haven't really used it much...it might simply be that i'm too lazy (busy?) to learn how to properly use it.

I would love to hear from people about how they digitally manage information. Please drop a comment.


image above from here

Blogging in 7 minute increments

I haven't blogged in a while -- it's been really hectic around here. But, I finally have some free time...the only catch is that in comes in increments of approximately 7 minutes in duration. I am spending the next few nights dating some detrital zircons on the SHRIMP. A couple of months ago, I posted about this avenue of research here. Each grain takes about that long to cycle through...there's a few numbers to be checked and recorded, and then you move the beam on to the next grain.

The good news is that colleagues in my research group are willing to help me out with this analysis. The bad news is that since the machine runs 24/7 and they are my samples, i'm the one who gets to sit here from 7pm until 7am....good times. I don't mind working the graveyard shift, but I really have a hard time the first night...once ya get into the groove it's not so bad. There is something a little strange being opposite from the rest of society though. One of the several random jobs I worked during college was as a night watchman -- it is definitely a lonely existence. Some people work these hours for years and years...I don't know how they do it.

Anyway....hopefully, I'll have a chance to catch up on the latest in the geoblogosphere....in 7-minute increments.

Day in the Life

Lab Lemming and Highly Allochthonous decided to answer the question: "What do scientists actually do?".

See what they do on a typical day here and here.

For me, not sure this is a typical day...it's Friday and I just finished a draft of a long paper 2 days ago and gave to advisor. But here goes anyway...

8:15-8:50: train ride into office
8:50-9:25: check email and make blog post about French turbidites
9:25-10:00: chat with colleague on phone who just started a tenure-track position this month, discuss possible future collaborations
10:00-11:15: update spreadsheet database and associated plots with new radiocarbon ages for Holocene sediments offshore southern CA; get excited about how well-constrained this basin is temporally
11:15-11:45: chat with colleague on phone about the above; directions to go for writing it up
11:45-12:20: lunch
12:20-2:00: research possible job opening; start application process
2:00-2:15: get information together for rock samples I need to start processing next week
2:15-2:45: look for said rock samples in inefficient and messy storage area in the attic of building i'm in
2:45-2:50: have a little freak out moment when can't find rock samples (they are all the way from South America!)
2:50: remember I already put them aside right under my desk...phew
2:50-3:40: search for paper online that i've been meaning to look at; found it and read abstract, intro, and looked at figures
3:40-now: write this blog post
after now-later: go home and go out to dinner with girlfriend and another friend in San Francisco

Pretty easy-going day all in all

Procrastination

In an effort to not do any work, but still sit at a computer pretending i'm working...i've spent time updating and modifying this blog with a new look and more links at the side.

A fellow geo-geek from Stanford (now a post-doc at Syracuse) has a nice blog called Apparent Dip ... check it out.