Saturday, September 29, 2007

GradU asking for money...

Well my GradU has hunted me down and is now asking for money since I am now an alum. They have a whole bit trying to make it seem as if alumni donatins helped pay for my graduate studies. What a load of bull****.
Facts:

1) My first three years I was on a training grant that my department got from the NIH. It paid for my tuition, my stipend, and my health benefits for the first three year.

2) After that my Grad Advisor's grant covered all that.

3) Yes that included tution- a real racket since after my first year I took only one course (in my second year).

4) What was I doing instead of taking classes? Mostly working away in lab which brought a couple publications and helped my PI renew his gratn. I did work as a TA as well but I was providing a service and getting compensated accordingly.

5) Overhead at GradU hovers just below 65% so in theory the space, electricity, etc. I was using in lab was being paid for. The lab consumables was being paid for by my PI's grant. Oh by the way GradU charged labs for internet access above overhead, the same for phone service. Tuition in other words was gravy. The tuition is waived for those in the humanities and GradU doesn't charge for internet access in their offices.

6) GradU was constantly finding ways to try and cut costs that required us grad STUDENTS to do more work that used to be done by paid university staff.

Alumni donations did not really help pay for my education. They did pay for part of the building I worked in but a lot of the costs were paid for by grants.

Needless to say, I really don't feel I owe GradU anything. Maybe if the department asks for money since they don't recieve much from the university (got to keep costs low, don't want to spend that overhead on the department generating it. Much better to pay for a new Dean of something or other whose job it is to look to make sure the University it extracting as much overhead as possible while providing the least amount of service. For a brief period of time they cut back on trash pick up in the labs. That did not go over well.

Got to love a university run like a company.

Monday, September 24, 2007

What's Up, Postdoc? September Carnival...

Hi all,

Sorry for the slight delay in posting. Really enjoyed reading what everyone has posted - always informative and fun. In keeping with this month’s theme, maybe some of you can give me advice on how to be a great blogger while keeping up with life and lab.

On to the What's Up, Postdoc?">September Carnival...

Given the numerous professors (Chad at Uncertain Principles, Steve Hsu at Information Processing, Larry Moran at Sandwalk, T. Ryan Gregory at Genomicron, and PZ Myers at Pharyngula to cite a few) talking about the not so great academic job market for those in the sciences, this month’s theme of advice seems very appropriate especially as we try to stop being pawns of science. Schlupp at I postdoc, therefore I am, Alex at The Daily Transcript and I at the Ponderings of a Fool all talk about the market with the advice being know what you are getting into. Laura, The Geeky Mom, brings up another important point, do what you love.

That advice is reiterated to those joining labs this fall. Lou at A Scientist’s Life has 9 points for those new graduate students and post-docs. The Mad Hatter at A Mad Tea Party advises that you shouldn’t postdoc unless you are doing it for the right reasons. Want to know the wrong reasons? Read the post. The Propter Doc has a 4 points for picking the right project as well as advice for getting advice from a senior member in the lab. Jenny F. Scientist tells it straight to the new graduate students.

Of course once you are in a lab, advice is useful. Sunil on Balancing Life points us to what the recently departed Daniel Koshland had to say about scientific discovery, The Cha-Cha-Cha Theory. Sometimes the advice in lab is amusing as Jooyla, who is N@ked Under her Lab Coat, discovered.

Lab work eventually leads (or so we hope) to writing. Sometimes the writing just doesn’t happen. Brad at The Unbearable Lightness of Being a Postdoc advises how to overcome writer's block. The Incoherent Ponderer discusses what do when a co-author goes MIA jumping of from a post from Female Science Professor. Schlupp goes into writing from the sidelines.

Not all communication is to those in the sciences. Black Knight and Bayman delve into the need to explain sciences to the rest of the public.

Dr. Brazen Hussy asks and receives advice about applying for a dream job in which she also gives advice on finding jobs. Getting that job requires an application with a CV. Incoherent Ponder weighs in on whether to tweak or not. Ms. PhD gets varying advice on perfecting your CV.

The Incoherent Ponder cautions us all to think before we send that e-mail.

And a post by Day By Day reminds us to take that break from lab in the here and now.

Thursday, September 20, 2007

September carnival...

The September Postdoc Carnival will be pushed back to September 24th! I now have a presentation Monday morning, so everyone will have an extra day to get submissions in!

The theme will be advice.

Of course all other topics related to being a postdoc will also be gladly accepted.

Links to the submissions can be sent to postdoccarnival "at" gmail "dot" com or ponderingfool "at" gmail "dot" com.

Happy blogging!

PF

Saturday, September 15, 2007

Cheaters and casting doubt...

The New England Patriots were caught cheating. The rules clearly state that teams should note tape other teams in the manner the Pats did. The Pats did exactly that. This was after the NFL sent a letter to all the teams reminding them of the rule because of suspicions that the Pats had done that last season against the Green Bay Packers. The NFL fined the team $250,000, the head coach, Bill Belichick, $500,000 and took a draft pick away from the team (a 1st road pick if the team goes to the playoffs this year). John Clayton, Don Banks, and Peter King all weigh in on why it was not enough. You also have this from Dr. Z:
"Marinelli was the defensive line coach in Tampa Bay when the Bucs beat the Patriots in the 2000 regular season opener and did a good job controlling New England's offense. After the game the Patriots' offensive coach, Charlie Weis, was overheard congratulating the Bucs' defensive coordinator, Monte Kiffin.

"We knew all your calls, and you still stopped us," Weis said. "I can't believe it.""

We will never know if Weis was being completely honest or just exaggerating for effect (i.e. whether they were cheating then or not) but the cloud will hang over the Belichick era of the Pats. If I were Norte Dame, I would take pause that is for sure.

The cloud that hangs over the Pats though does call into question their three Super Bowl victories under Belichick. ESPN is running a story on the Eagles who played the Pats in the latter's last Super Bowl victory and them questioning whether signs were being stolen in that game where the Pats had an uncanny ability to call screens whenever the Eagles were going to blitz. This could be just good play calling or it might be an indication of something else.

Lets take a look at those three victories:
2005: Pats 24, Eagles 21
Score going into the 4th quarter? 14 to 14.
2004: Pats 32, Panthers 29
Score going into the 4th quarter? 14 (Pats) to 10 (Panthers) The Pats won a field goal with 4 seconds left in the game.
2002: Pats 20, Rams 17
Score going into the 4th quarter? 17 (Pats), 3 (Rams) The Pats won on a field goal in the remaining seconds of the game.

All three games were slim victories. The first game was the only game that was not close going into the final quarter. Knowing the signals would be the difference in these games, especially when you consider two of those games all the offense needed to do was maneuver into field goal position.

That is not to say the did cheat but it does give one pause and why so many associated within the NFL are taking it so seriously. Such a level of cheating possibly determing who wins the Super Bowl is a big deal. Pro Football is a multibillion dollar business. This calls into question the outcome of who wins the champsionship. The largest sporting event in the US.

Monday, September 10, 2007

On tenure again...

Dean Dad talks about junking tenure maybe replaced by a series of long-term contracts. His perspective is from being an administrator at a community college. It might make sense there, I don't know enough to comment. With regards to research universities though for those in the natural sciences it is absurd.

Why? Science faculty already have to stay competitive in order to keep getting grants. The grants pay for the research, internet access, going to conferences, having students and oh yes part of their salaries. In other words they are already competing and staying productive. Of course in exchange for giving up tenure, universities would have to give up something-money. After 5-7 years of being a grad student and then spending another 3-4 years as a post-doc and then 7 years at an institution as a junior faculty member, scientists want a little security. Lowering the security means universities would have to pay significantly higher salaries. Given the nature of contracts and the competition involved there would be bound to be more movement than there is now leading to more expenses. Would the university really gain that much more? Science faculty already have to stay productive. The difference in overhead dollars brought in would be minimal and that is what the university wants hence that is the primary determinant in getting tenure. Most likely universities would be unwilling to pay for giving up tenure. Without the increase in pay, it would be silly for faculty to give up on tenure. It is a no go. It would get faculty to be better teachers. Under certain scenarios it would actually favor faculty focussing more on research than being good teachers/mentors.

Sunday, September 9, 2007

PAUP Help...

I have been running phylogenies and have been having this problem with PAUP running maximum parsimony where it is supposed to find the 1000 most parsimonious trees.

Elapsed Taxa Rearr. -- Number of trees -- Best
time added tried saved left-to-swap tree(s)
33:22:11 - 247089521 1000 628 223551
33:23:11 - 247154671 1000 627 223546
33:24:11 - 247315353 1000 627 223546
33:25:11 - 247430339 1000 627 223546
33:26:11 - 247587809 1000 627 223546
33:27:11 - 247713071 1000 627 223546
33:28:11 - 247815620 1000 626 223543
33:29:11 - 247946647 1000 626 223543
33:30:11 - 248070084 1000 626 223543
33:31:11 - 248213054 1000 626 223543
33:32:11 - 248347299 1000 626 223543
33:33:11 - 248481072 1000 625 223543
33:34:11 - 248565681 1000 625 223543
33:35:11 - 248698430 1000 625 223543
33:36:11 - 248808469 1000 625 223543
33:37:11 - 248972895 1000 625 223543
33:38:11 - 249090122 1000 625 223543
33:39:12 - 249167303 1000 691 223543
33:22:11 - 247089521 1000 628 223551
33:23:11 - 247154671 1000 627 223546
33:24:11 - 247315353 1000 627 223546
33:25:11 - 247430339 1000 627 223546
33:26:11 - 247587809 1000 627 223546
33:27:11 - 247713071 1000 627 223546
33:28:11 - 247815620 1000 626 223543
33:29:11 - 247946647 1000 626 223543
33:30:11 - 248070084 1000 626 223543
33:31:11 - 248213054 1000 626 223543
33:32:11 - 248347299 1000 626 223543
33:33:11 - 248481072 1000 625 223543
33:34:11 - 248565681 1000 625 223543
33:35:11 - 248698430 1000 625 223543
33:36:11 - 248808469 1000 625 223543
33:37:11 - 248972895 1000 625 223543
33:38:11 - 249090122 1000 625 223543
33:39:12 - 249167303 1000 691 223543

The number of trees left to swap went up and rapidly went from 691 to 975 at last check. Has anyone had that happen? I haven't seen it before and trying to make sense of it. Any help would be greatly appreciated.

Thanks!

Septemeber Postdoc Carnival-Submissions

The September Postdoc Carnival will be on September 23rd! I (the Pondering Fool) will be hosting.

With the start of the academic year & the scurrying around of new/returning students, the theme will be advice (that could be to an undergrad, a grad student, a new postdoc, etc.).

Of course all other topics related to being a postdoc will also be gladly accepted.

Links to the submissions can be sent to postdoccarnival "at" gmail "dot" com or ponderingfool "at" gmail "dot" com.

Happy blogging!

PF

Sunday, September 2, 2007

Blogger day (a day late)...

On the 1st was Blog Day 2007. It is a day in which bloggers direct their readers to other blogs which the author likes to read.

Here are my five:

Anterior Commissure - A talented graduate student "exploring the intersection between hormones, brain, and behavior." She also delves into communicating science. Very prolific blogger (especially relative to me). Wonderful discussion of science.

Minor Revisions - A post-doc discussing life. Always a great read. Stories I think any of us in science can relate to on some level or another.

Incoherently Scattered Ponderings - A physicist who has gone from being a post-doc to an assistant professor. Always an interesting perspective on things. Very educational for those who want to know about that initial stages of being a faculty member.

Dr. Mom - Another person who has been making the transition from being a post-doc to being a productive faculty member. Always excellent for those wanting to know about starting the tenture trek.

On Being A Scientist and a Woman - Another recently hired faculty member thus completing the triology. Wonderful reads on being a scientist, a daughter, a mother, a wife, a woman, a person starting to set up a lab.