Archive for: January, 2010

Notes from an advisor's desk

Jan 29 2010 Published by under Uncategorized

My undergraduate advising duties have picked up quite a bit over the last few months. I've had a bunch of meetings with students in their second through forth year and every meeting is different. I didn't expect that a group of people all going through the same (or similar) training would have such completely different experiences, but perhaps that's a simplistic view.

In about five minutes I can tell whether the student is just there for affirmation that they are on the right track or if they came because they don't know how to get to the end game. Initially I was surprised how many students are in the latter category (the major requirements and spelled out in multiple places, with worksheets to help students schedule their classes), but then I remember that most of the students I see are younger than 20 and are choosing their own path for really the first time. In high school their schedule is predetermined for them, for the most part, but now they are free to follow guidelines or not, with no consequences to those choices until after the fact. From my position now it seems crazy that students can't stay on track to meet the major requirements in 4 years, but I was a wide-eyed student once too and many don't know exactly what they want to do from day 1.

In my capacity as an advisor I try and get to know what they want to do post-university, and within reason, put them on a path to succeed. But I have been surprised at my reaction to the various students who walk in my office. In most cases the meeting is straight-forward and I give them a plan for a year or two of classes. In about 40 minutes I can work them through what they need to do and we can agree on a course of action. What intrigues me, however, are the students at the extremes of my reaction spectrum. Some walk in and I find a pretty limited desire to help them. I'm not saying I don't work with them, but something about our interaction keeps me focused more on how to get them done with the major rather than tailoring it to their specific interests. In other cases I have gone out my way to come up with a ideal schedule for students, including finding lab work for a student who didn't even know that option existed. I only recently realized that there was a bell curve to my advisee interactions and I haven't been able to pin down what the factors are that influence it, because it is not related to GPA, the engagement of the student, or other potentially obvious factors and I'm meeting them all for the first time. Some students are just more helpable than others and I guess sometimes I'm just a sucker for a good story.

4 responses so far

Inviting Chaos

Jan 27 2010 Published by under Uncategorized

No, this is not an overt attempt to get Prof. Chaos to let us know how things are going in her world of babies and tenure decisions (as far as you know...), but the continuation of an on-going saga for me. Back when I first started the lab and the blog I posted (here and here) about my quest to have some old data sent to me by a PI who never published them and no longer was in a position to complete the work. My initial contact with Frustrating Potential Collaborator was positive, but without warning FPC fell off the map. I tried to re-initiate contact. Oh, I tried. To no avail.

Late last year a friend of FPC told me that FPC was now interested in talking to me about the data gathering dust. At the time I blew that off because I had already duplicated some of the work and didn't feel like another round of get-screwed-by-the-old-gaurd. But we got some data back recently that just screams to be compared to the data gathering dust that we haven't already duplicated, so I had to chose between contacting FPC again or blowing many thousands of dollars and lots of time for the same results. I thought I should try the "easier" route first.

Well, so far so good. I had an email conversation last night with FPC and they have agreed to release the data to me. It's not clear how much they have (it appears to be far more than I had originally suspected), but so far we have the green light. BUT, twice already I have asked about what would be expected when it comes to authorship and involvement in the final product and twice those questions have been ignored. FPC is now retired and appears not to care what we do with the data, but there were students involved in those projects who have gone on to other things and who might like to see those data published. None of the people in question are still in academia, so tracking them down is difficult.

As excited as I am to get the data and start to work with them, there are alarm bells going off in my head that there may be far more strings attached to the data than I can see right now. But if FPC gives us the okay to go forward, what is my responsibility to FPC's former students from more than a decade ago? I will try and pin FPC down in terms of getting their consent, but if that doesn't happen does it blow up the whole thing? I'm not particularly comfortable with going forward without the consent of the other potential authors. I'll have to see how this plays out of FPC's end. I know that one student has been contacted, but I'm not sure about the others. The last thing I want is a bunch of interesting data that are stuck in limbo, but the possibility of getting a bunch of people who have been out of the game for a while involved in the writing or editing makes my head hurt even more.

Best case scenario is that the data are given to us with a list of a couple of people who should be included on the resulting papers, but who want nothing to do with the process. But best case scenario is usually as likely as riding to work on a unicorn.

4 responses so far

Not exactly what I thought

Jan 26 2010 Published by under Uncategorized

I'm not sure what I was expecting, but my first day of class went differently than I had imagined. I got there early to set my computer up and of course found a closed cabinet that held the AV hook-up. Before warming up for my interpretive dance that was my back-up in case the slides didn't work, I checked with the desk at the nearby computer lab. Yes, they had a key. Yes, they would open it. As the Guy With the Key went to unlock the cabinet, he pulled the handle to reveal that it was unlocked and that I am a dumbass. Luckily, I am used to that.

The classroom is set up in the most awkward arrangement possible, with the closest desk only feet from the screen and the computer not even close (thanks for the 3 foot cord!). The result is that any hope of using "presenter tools" to see what is coming up next is completely lost. Yet another drawback to modifying someone else's slides for a lecture.

For some reason, the students waited outside and almost all came in at once about 3 minutes prior to the class's start. All but one of them completely ignored me standing two feet from the door and telling them to pick up a syllabus. They grabbed the paper but regarded me in the same way that most walk by someone asking for change on the NY subway.

That trend continued into the lecture, where questions for them to answer were greeted with a zombie-movie-just-before-someone-gets-attacked kinda quiet. If I hadn't forced them to introduce themselves part way through the class I would have been wondering whether I had the statistically-impossible fortune to preside over a class of people entirely mute. I tried to toss a couple of off-hand jokes out there - nothing. I asked questions - nothing. If there were crickets in the room it would have been a full blown cliche. I really had to pin them down to get any response. I'm thinking of releasing a slightly shaken ferret into the class on Thursday.

Other than that, it was fine. I kept it fairly brief, talked about what I expect of them and what they can expect of the class. I introduced myself and the subject and they were out of there 30 minutes early. Three showed up late, but only one was really late. I only had one person obviously texting in class and I'll try and find a way to address that.

They seem like a decent group, hopefully I just need them to warm up a little.

15 responses so far


Jan 25 2010 Published by under Uncategorized

Having to do most of your Tuesday lecture on Monday morning: likely to be typical.

Being a little nervous about getting the first class right to set the semester off: not surprising.

Having the car not start on Monday morning: my life.

I guess I should be glad that it's not tomorrow before class, but seriously. I just blew more than half my day waiting for a tow truck and going to the dealer only to have them tell me they can't find anything wrong with it. Why don't we start with the fact that the engine sounds like I filled it with buck shot instead of gas once we finally did get it to start. The car is less than a year and a half old and never given us any hint of a problem. This morning it's dead in the driveway?

Now I have to finish my lecture, make sure the syllabus is coherent and probably find some time to visit the room I am teaching in, which is clear across campus, all in less than half the time I had planned. Shit just never gets boring around here. Why do I feel like we're in for some projectile vomiting tomorrow morning as we're dropping the Wee One off? Nothing like teaching the first class covered in vomit.

6 responses so far

Friday Finale

Jan 22 2010 Published by under Uncategorized

We just got back some really important data and immediately found what we were looking for. With my luck I'm sure there is something wrong with it, but for right now it's the first solid piece of data we've gotten back from our dependable Major Data Producing Center. These same data in another system have taken one of my students almost a year to produce in another way, so this is a welcomed turn of events and gets us damn close to having everything we need to write a paper.

The first piece of good news we've had in a while. A good way to go into the weekend. In which I will be here analyzing these data.

8 responses so far

Brought to you by the letter M

Jan 22 2010 Published by under Uncategorized

WTF is up with the states that start with M this week? First Massachusetts goes out in a election of artificial national importance and elects a complete jackass of a senator who announced in his victory speech "My daughters are available, but if I have my way, health care won't be." Stay classy, senator! Since one of his daughters in engaged (and clearly weighing that fallout of punching her dad on national television in this video of the speech), I'm not sure what that means for the future son-in-law or health care.

Next up is a tandem of Mississippi and Missouri, both of which have introduced anti-evolution bills jam packed with the same tired old language that has been knocked down by the courts time and time again. The Mississippi bill tries "To require that the lesson have equal instruction from educational materials that present arguments from both protagonists and antagonists of the theory of evolution." Hmmmm, never heard that one before. Way to get creative Mississippi.

Missouri takes a more indirect approach by couching the bill's language to make it seem like they are all about the science by saying

"teachers shall be permitted to help students understand, analyze, critique, and review in an objective manner the scientific strengths and scientific weaknesses of the theory of biological and hypotheses of chemical evolution"

and following it with

"This section only protects the teaching of scientific information and this section shall not be construed to promote philosophical naturalism or biblical theology, promote natural cause or intelligent cause, promote undirected change or purposeful design, promote atheistic or theistic belief, promote discrimination for or against a particular set of religious beliefs or ideas, or promote discrimination for or against religion or nonreligion. Scientific information includes physical evidence and logical inferences based upon evidence." as a really nice disclaimer.

But, dear Missouri, if your teachers are teaching science, they should already be giving students the idea that scientific hypotheses and theories are always being tested by evidence-based research. Some, like evolution, hold up to everything we throw at it, even if we are occasionally surprised at our lack of understanding of the processes involved. Why would you need a House Bill to affirm this, and why specifically bring up evolution? Oh, maybe this little gem:

"Neither the state board of education, nor any public elementary or secondary school governing authority, superintendent of schools, or school system administrator, nor any public elementary or secondary school principal or administrator shall prohibit any teacher in a public school system of this state from helping students understand, analyze, critique, and review in an objective manner the scientific strengths and scientific weaknesses of biological or chemical evolution whenever these subjects are taught within the course curriculum schedule."

Oooo, an immunity idol for anyone who wants teach delusional drivel! How convenient. I have to admit that this bill is well crafted to try and side-step as many bullshit alarms as possible, but the intent couldn't be more clear. This is not a bill to protect that biology teachers who are trying to teach evolution in a hostile environment. The bill's sponsor, Robert Cooper (R*) has put forward over half a dozen previous anti-evolution bills, but luckily his success rate is about as good as mine with grant proposals.

The bar has been set high Montana? Whachugot?

*I know, total shocker. I would never have guessed that this was a Republican-sponsored bill.

3 responses so far

Not even wet yet

Jan 21 2010 Published by under Uncategorized

Here I am finishing up my Syllabus for teaching this semester and I am already being hassled about teaching in the fall. I don't have anything that I am responsible for in the fall, so my options are either to design my own course or teach an existing one. By "teach an existing one" I mostly likely mean teach a section or part of a section of the mega intro course. There's pros ad cons to both.

Teaching my own course would mean that I could control all the content and teach only what I want to. It would also mean that I would take on fewer students (probably 30ish). BUT, there is a push right now avoid developing specialized advanced course, and instead target new courses at hooking freshman into science. Therefore, I would be building a course that would be taking research from my field and applying to what freshmen understand. On the surface this sounds easy, but in practice it might completely suck.

Being propped up in front of 300 or so students to teach an intro course is not my idea of fun, but the material is all laid out already and it would require 1/10 the preparation. I also wouldn't have the grading to deal with that would result from a smaller course and it would tick the "taught a big class" box in the departmental mindset of what people need to do before tenure. This is not something I feel I have to check off at this point, so this is a minor advantage.

Having not taught either type of course, I don't know what the time commitment is for each, but I would assume that the larger course that is already laid out would be less. Thus, I am tempted by the path of least resistance on the teaching front. OTOH, a smaller course of my design would clearly be more fulfilling and make the Dean happy because it fills the New Teaching Mandate that is being pushed.

Maybe I'll flip a coin.

8 responses so far

NFL Challenge OT

Jan 19 2010 Published by under Uncategorized

I've let the NFL playoffs and the cage match between DGT and Nat (Who tied during the regular season of the SciBlog NFL challenge) slip through the cracks a bit. That may be a good thing since their picks for round one were fairly dismal, with each guessing just a single game of the four played. Prior to last weekend I asked them both to pick straight through the Super Bowl to determine that end-all champion. The picks are as follows, winning team in CAPS:

Divisional Round

Chargers over JETS (0)
COLTS over Ravens (1)

SAINTS over Zona (1)
Dallas over VIKINGS (Traitor!) (0)

Confrence Round

Colts Win

Dallas Win

Divisional Round

Chargers over JETS (0)
COLTS over Ravens (1)

SAINTS over Zona (1)
Dallas over VIKINGS (0)

Confrence Round

Chargers Win

Saints Win

Interesting that the picks from last weekend cancel out put the picks for this weekend are completely different. Super Bowl picks to be announced closer to the game.

One response so far

Burnt or fried?

Jan 18 2010 Published by under Uncategorized

I have been, more or less, writing for the last four months. Book chapters, grants, pieces of manuscripts and pieces of other grants. It's been pretty non-stop and I've kept chugging along. The past month, in particular has been a really good time to finish up a lot of things because there's so few people to bother me at work until next week, when the semester comes crashing down again. But I have two more small pieces of writing left to do before then and all I can do is just stare at my computer. It's like I accidentally shifted into neutral while driving and now the gas pedal doesn't do anything but rev the engine.

I am also supposed to be planning for my course that starts next week, but I have no sweet clue how to do that because this is all new to me. I'm going to go through all the materials that were given to me and make changes where I see fit, but otherwise I'm at a loss as to what to do in order to "prepare". It's like asking someone who has never really cooked to prepare to make a meal for 40. I'll just start by washing the vegetables and then...

Remember when the concept of the holidays meant that you had time away from work to recharge? Now it feels like a flurry of getting work done during the time when fewer people are around to suck your time away. I'm now heading into the new semester when I am teaching undergrads for the first time, already feeling like I've been run over. I still have 8 days until my first class, I'm sure I'll get myself sorted before then.

11 responses so far

The Phylomon project: Biodiversity or Megafawning?

Jan 15 2010 Published by under Uncategorized

In a post last night, the venerable Dr. Isis brought the Phylomon project to the attention of her readers. As an individual interested in biodiversity, I thought I would check it out. In principal I like the idea and the creators described it as such:

“What is this?” you ask? Well, it's an online initiative aimed at creating a Pokemon card type resource but with real creatures on display in full “character design” wonder. Not only that - but we plan to have the scientific community weigh in to determine the content on such cards (note that the cards above are only a mock-up of what that content might be), as well as folks who love gaming to try and design interesting ways to use the cards. Then to top it all off, members of the teacher community will participate to see whether these cards have educational merit. Best of all, the hope is that this will all occur in a non-commercial-open-access-open-source-because-basically-this-is-good-for-you-your-children-and-your-planet sort of way.

But, besides just bringing attention to the project, I would like to encourage readers with some artistic talent* and familiarity with non-animal creatures to get involved. My issue with 99.5% of "biodiversity" projects is that they are anything but. Most are exclusively devoted to animals, or if they really get crazy, metazoans (including insects and squishy creatures mostly in the sea). There may be some value in showing people all the charismatic megafauna that Must Be Saved, but it does not serve the greater purpose of introducing people to biodiversity in the real sense. The Discovery Channelization of nature has value, but it's kinda like reading People magazine to get all your news.

Figure 1. A slightly dated classification of eukaryotic biodiversity. Animals are bit players in the grand scheme. It's a big world out there folks, if you really want to understand biodiversity look up a few of the subgroups on this tree.

I bring this up because people associate the need to conserve biodiversity with warming polar bears or Madagascar lemures with no trees to climb, but the reality is that biodiversity is lost under your very nose no matter where you live - it just happens without much fanfare. No one cares when runoff from a golf course obliterates the diatom community in a local pond or a fish farm wipes out a coastal community of organisms. As long as there are no turtles to go belly up, we're good.

So artistic readers, find an unusual bug to add to the phylomon project. Draw a dinnoflagellate, ciliate, apicomplexan or trypanosome. If it's for the gaming community (which they suggest is a target audience), then what could be nastier than the dinoflagellate saxitoxin, a neurotoxin 100000x more potent than cocaine? Apicomplexans cause malaria and toxoplasmosis, just to name a few diseases they are responsible for. Trypanosomes are responsible for African Sleeping Sickness and Chagas disease, and ciliates are voracious predators and parasites. Do an image search for any of them and you'll be shocked at the diversity in form and function.

The unicells of the world control where and how multicellular organisms live. Maybe more people should be aware that they are out there.

*My lack of artistic ability is so great that I make others around me less artistic. My daughter won't even acknowledge the likeness of Elmo when I try and draw him for her, and he's just a couple of circles and a mouth.

2 responses so far

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