Saturday, December 29, 2007

BCS Nightmare II...

So the BCS title game pits Ohio State (11-1) vs. LSU (11-2). A team with two losses could be the "national champion" of college football (well of the BCS division, aka the division formerly known as 1A). This would be a nightmare for the BCS. Why? Well those Warriors of Hawaii. They are currently undefeated. They play Georgia in the Sugar Bowl. If Hawaii wins, they will be 13-0. In other words they would have done what no other team in the division formerly as 1A could do this year, win all its games. You then throw in the other teams with two losses and you could have really muddled situation. Here are my rooting interesting this BCS season:

Rose Bowl: USC v. Illinois - Got to go with the Pac-10 here. Plus, USC would have two losses (see above why that matters). If they blow out Illinois and LSU barely gets past OSU in the title game then how can you really argue that the Trojans shouldn't also be thought of as national champs?

Sugar Bowl: Hawaii v. Georgia - The Warriors of Hawaii as discussed above.

Fiesta Bowl: West Virginia v. Oklahoma - Going to go with the Mountaineers. Why? Why not. Both teams have two losses.

Orange Bowl: Virginia Tech v. Kansas - Going to go with Virginia Tech. This would move Kansas to two losses and keep Tech with only two.

BCS Title Game: OSU v. LSU - LSU.

If all of the BCS games go the way I hope this will be the end of the season records:
OSU 11-2
LSU 12-2
Kansas 11-2
Virginia Tech 12-2
West Virginia 11-2
Oklahoma 11-3
Hawaii 13-0
Georgia 10-3
USC 11-2
Illinois 9-4

This would be beautiful!

Wednesday, December 26, 2007


Well it has been a bit. I have been "productive". I submitted two journal articles and a review. The journal articles were sent off of a month a half ago. The review was submitted on Friday. Last week, I also got the comments on one of the articles I submitted. The reviewers thought the paper should be published pending revisions of clarity and to address their ideas (or lack thereof). Incorporating their comments did improve the paper which is good. The only problem was my PI wanted the revised manuscript submitted on Friday as well. Of course the PI (who I do like and is usually good about work/balance) had to go home (significant other wanted PI home by a certain hour, so did mine but I am not as high up on the totem), so it was me submitting the review and then the revision. Now they are off. Of course, they are sitting there. PI was hoping someone this week would look at them. I don't think that is going to happen. We shall see. The other paper is still listed as "under review" so hopefully I hear something in the new year. If it was to be rejected I would think we would have heard by now. It is much easier to reject outright than accept/accept pending revisions. We shall see on that. Hopefully it is fine. At the very least no new experiments. I have moved on to two other projects with the goal to get them finished and manuscripts submitted before my wedding in July. I can be slightly crazy like that. I hope to apply for faculty positions in the fall so two more papers would be fantastic. I will be an author on another article hopefully submitted before the spring, but I won't be a first author but rather a contributing one. So it will be a busy new year but I do resolve to blog more. It is good therapy as is reading all the wonderful other blogs out there. Happy End of 2007 CE to all.

Saturday, November 24, 2007

Rooting interests or the BCS nightmare scenario...

LSU, who was ranked number one in the BCS rankings, lost last night to unranked Arkansas. This sets up the nightmare scenario for the lords of the BCS as the Warriors of Hawaii kept winning (they are 11-0 now). If this week Missouri beats Kansas, UConn upsets West Virginia, and Oklahoma St. beats Oklahoma, and Missouri then looses next week in the Big-12 championship game it would mean Ohio State at 11-1 would be number 1 and going to the championship game. Number two would be unclear but most likely it would be a team with two losses. The same scenario can come to be if West Virginia wins this week but then looses to Pitt next week. In other words a team that has lost twice in a season would be going to the BCS Championship Game over Hawaii, a team, if they beat Washington next week, that went undefeated. Kansas under this scenario would have only one loss and would also be out of the big game. The BCS would be shown to be the joke it is.

Besides how do you pick one two loss team over another? How it is set up now, if a team lost two weeks ago would be in better shape than one that losses this week or next (including one that would have only one). It is absurd.

Monday, November 19, 2007

Sociobiology, evolutionary psychology and Chimps. Oh my!

Over on Evolving Thoughts, John Wilkins is going to make the case for sociobiology. He starts out by distancing sociobiology from evolutionary psychology taking the position the latter takes an overly adaptationist view of evolution. It should be interesting to say the least.

What I am still waiting on is to find someone to discuss the article published in PNAS a couple weeks ago entitled Phylogenetic analyses of behavior support existence of culture among wild chimpanzees. The authors, as summed up in the commentary by Andrew Whiten accompanying the article, "conclude that the phylogenetic trees that best describe the affinities between the behavioral profiles of different chimpanzee communities are not compatible with a genetic explanation and instead support the cultural interpretation." In other words, Chimps might have social learning and the cultures that go with that. An interesting question is then, did the last common ancestral ape of Chimps and humans also have social learning/culture? If so, how does that impact how we view human evolution? If yes, then the evolution of humans in terms of brain development/intelligence/behavior/etc. must be looked at in both a biological and social context (really the interplay between the two).

Thursday, November 1, 2007

Remember in '08, Vote Colbert!

Colbert's campaign is over before it really began. The Democratic Party in South Carolina has decided not to allow Colbert to be on the ballot in their Primary. He paid the fee ($2,500) but they have the option of not letting him enter if they don't think he can win.

I have to say given they have that option, why do they charge a fee? At least it is not as crazy as the GOP. The fee for them is $35,000. Talk about crazy! Forget about paying for a campaign, someone who is working class can't get even in the game for the two major parties.

Just for this my vote for 2008 is going to be a write-in: Stephen Colbert. I encourage others to do the same. The system isn't broken, it is just set-up in a manner that isn't for, of and by the people. Colbert is a vote for pointing out the absurdity of it all in a nation that tries and sells itself as a democracy.

For those of you thinking you will be wasting you vote, REALITY CHECK you usually are wasting your vote in a presidential election. The way the electoral college works means if you are in a solid Blue or Red state, it doesn't matter who you vote for. Even in "swing" states the margin of victory is so significant in actual number of votes that you choosing to vote Colbert isn't really going to matter. Look at the numbers and think. Your vote is already being wasted. If that is the case, why not send a message? What do you have to lose? I say vote Colbert in '08! Write him in. Send a message!

Wednesday, October 24, 2007


Sorry for the lack of updates. I have been busy preparing three articles.

One was relatively easy. Our collaborators are writing the majority of the article. I just had to write-up the results I got along with the methods associated with them. Sent it off and it is in their hands now.

The other two papers though are of my own data. The plan is to have them printed back to back in Journal of Cool Stuff. Paper 1 is on the wet lab work I have done to understand MyFavProtein. It went through multiple revisions beforing going to the Advisor. The Advisor did not like it. Some of his comments made perfect sense and have greatly improved the article. Other comments contradict what I learned in the last couple of papers I wrote with my Advisor. It is maddening.

For example, in previous paper we ended the introduction with a paragraph stating what the paper is about, laying out the basic questions answered. Advisor for that paper thought I did not provide enough details in that paragraph. It ended up being like the abstract but without all the numbers. Given that, I wrote the last paragrpah in the intro of the current paper in a similar manner. The Advisor's response? Cut it- stating that you shouldn't put in any details which is a complete reversal of the Advisor's previous advice. What is a post-doc to do?

The 2nd article is computational work I have done, placing those results into context with the known experimental results. This is the first time I have written such a paper. Needless to say the actual writing of this paper is not easy. I have a draft finished. It currently is sitting on the desk of a fellow post-doc in the lab who is trained in said computional analysis. This other post-doc is extremely laid-back. You have to constantly stay on him/her otherwise things never done. Unfortenately for me, he/she has a backlog of work for others that take priority over mine, so I wait. In the meantime, I work on figures and table, looking at a computer screen all day. No fun!

Once the articles are out it is on to writing a review. It doesn't end!

Thursday, October 11, 2007

Give a little and help improve science education...

Many of the fine folks over on Science Blogs are taking part in DonorsChoose Blogger Challenge. The money raised goes to directly helping science education in American schools. Many are for equipment that many districts can not afford to get on their own. It is a shame teachers have to beg for money but that is the system we have in America.

It is only getting worse under Bush but things really weren't that great under Clinton. Neither party really has a plan to deal with the disparity in funding for education in America. As long as we base it on property taxes, students living in poor districts are going to be behind.

The teachers behind these projects want to engage their students to critically think which is vital, many times through hand on learning.

So go DONATE and advocate for CHANGE - Do NOT accept things as they are!

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****.

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!


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.


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!


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.

Wednesday, August 29, 2007


Can I ask why does Bill Kristol keep going on the Daily Show? He has been on about 5 or 6 times. Jon Stewart uses him as a punching bag and he laughs along. I can see why the Daily Show keeps booking him, it is funny. Maybe Kristol enjoys being laughed at but there got to be better ways to have fun in life or maybe he is punishing himself for being the champion of the neco-con movement? I ask because it is just strange.

Tuesday, August 28, 2007

Posts to read...

The latest What's Up, Postdoc? is up on The Ways and Means of the Immune System. Check it out. Always a good read and Vero has done a great job!

Twice has the August edition of Scientiae. Wonderful posts are linked to so go read it!

A follow-up on the job prospects of those in the biological/biomedical sciences, here are some more posts on the matter:
The Daily Transcript
Sandwalk I Sandwalk II

Larry Moran at Sandwalk talks about how things should be and how is as an advisor as does Gregory on Genomicron. The problem is many faculty I have encountered are not like that. There are many talented graduate students and post-docs who do not have good mentors. Advisors who try and keep their trainees eyes only on becoming research faculty. That is not healthy. More must be done at the university level. The only problem is that their is no incentive for the institutions to actually do anything. Why rock the boat when you have plenty of overhead dollars flowing in? Especially when rocking the boat means spending some of that money?

To do...

In the next month and a half:

Need to write-up the last two papers from my thesis.

Figure out what adding Protein X to Protein Y as the latter modifies RNA Z does to the reaction.

With another post-doc write-up the results showing Protein X forms a complex with Protein Y especially when RNA Z is present based on those results whatever they are.

Finish biochemical characterization of an enzyme for our collaborators who solved the crystal structure of said protein and need my results to publish in a higher journal.

Turn 30.

Start new project studying if a certain metabolic enzyme from E. coli can be used as an antibiotic against a different group of bacteria.

With another postdoc, see if we can in an archaeal species replace an archaeal signature gene with a totally different bacterial gene whose gene product accomplishes the same task as the archaeal one and see if the replacement stresses the organism under various growth conditions.

Prepare a group meeting.

Start writing a review on thesis topic.

Today, doing the boring laying the ground work (i.e. purifying substrates) to do the experiments I want to get done while giving me the time to do the writing that needs to be done as well. What fun!

Thursday, August 23, 2007

Oh what great news...

Nature has an article on the data being released from the Federation of American Societies for Experimental Biology regarding the job market for those with PhDs in the biological and biomedical sciences (BBSs). The upshot is that the number of tenure track positions has pretty much flatlined since 1981 (hovering around 20,000) while the number of people receiving PhDs has increased to 7,000 in 2005. Needless to say most of those with a position are not leaving soon, creating a situation in which only 30% of those with PhDs in the BBSs have a tenure/tenture track faculty position (down from 45% in 1981). More and more, people are turning to industry (30%). The doubling NIB budget went towards many things, greatly expanding faculty positions was not one of them.

There is nothing wrong per se with PhDs leaving academia. People have different interests and talents. The problem is when you have graduate/post-doc advisors who cling to the idea of looking down at those that don't pursue a career in academia (usually narrowly defined as a faculty member at a research university). Those people are pushing an unrealistic set of expectations upon their advisees that is unhealthy. The numbers just do not support it. Anyone selling that notion is selling a pyramid scheme that primarily helps the advisor and his/her university & borders on "criminal" in my mind.

A PhD in theory should be about learning a set of intellectual skills on how to approach a problem, how to think and analyze data, etc. that can be applied to any number of career choices. That is a good thing. The US for one is a place that needs more people with scientific minds not less but realistic expectations have to be put forth.

What can be done? Well more money would help. Money to create more faculty positions while not increasing the number of graduate students a proportional amount. This would also create more competition between faculty members to attract students. This could only improve the quality of mentorship. In addition, create and pay for more higher paying research staff positions. There are people who are good researchers but are not cut out to be faculty members. Create room for those people. Let their skills be used appropriately Actually have career development staff at the university to aid graduate students and post-docs looking for positions outside academia. Really, why should faculty members have to carry this burden alone? Universities are getting overhead. It should be expected they then provide the proper resources for research labs. Career development without question fits there.

Undergraduate advisors also need to be more honest. Let those students thinking about attending PhD programs know the numbers and what is reasonable. Give them the knowledge they need to make an informed decision, that is your job.

We also need to improve the pay teachers receive. We need more science teachers teaching at the pre-college level. Make that a more attractive option. This also requires money to be spent on the resources to let science teachers teach well. Science is fun. Well thought out experiments are hands on learning. They get students to think, to learn and are significantly less boring than a lecture.

What else can be done?

Monday, August 20, 2007

The heat, oh the heat...

The dog days of summer seem to be lifting a bit. My energy is returning. Heat and humidity I do not do well in. I wilt. It is a little pathetic. Lab becomes salvation with its A/C and cold room. Of course, just because it is salvation doesn't mean I work anymore just means I become a blob appreciating the sanctuary. Blobs, well at least this one, do not write much. Part of that was because I did escape some of that heat and humidity for a bit. It is never enough though. Why oh why did I choose to do my post-doc here? Oh well. It is one of the downsides though of staying in academia - there isn't the same degree of freedom of choosing a place in the country or world to live. Jobs are tight, you have to be somewhat flexible in that regard. This was a deal-breaker for a classmate of mine in graduate school. She left science completely because of it. Only so much any person can sacrifice in the name of science.

Friday, July 20, 2007

Ummm anyone see something wrong with this?

CNN is covering itself and well makes itself look good. What type of society are we living in when a newscaster is being covered by the newscaster's news organization about doing his/her job? When we are all engaged in framing wars what becomes of actual discussion based on facts? Do we really want news organizations actively engaging in framing even more than they have in the past?

From Matthew Nisbet regarding framing and why more scientists should tap into it:
"That's the power and influence of framing when it resonates with an individual's social identity. It plays on human nature by allowing a citizen to make up their minds in the absence of knowledge, and importantly, to articulate an opinion. It's definitely not the scientific or democratic ideal, but it's how things work in society."

A new organization should not be the one's encouraging citizens "to make up their minds in the absence of knowledge". They should be the one's you know giving them knowledge. Isn't that their job?

Movie round-up...

Sorry for not posting. I haven't really had a good excuse other than writer's bloc. I have been enjoying the summer movies though that have come out. The blockbusters I have been overall more enjoyable than those that come out in late springwhere it was last in a trilogy after last in a trilogy or so it seemed. Though some of the "smaller" movies were very enjoyable. On to the latest batch of movies:

Ocean's Thirteen - Recaptures the charm of the first movie. The details of the plot are silly but the story knows that. It is all about the banter, the winks, the nods, the fun of having all these actors on screen together. It is Clooney's love letter to Vegas. Enjoyable, escapist fun.

Sicko - A well done Michael Moore documentary on the American health care system. Not so much about those without insurance but rather those with insurance & the rationed care they receive. The movie has numbers that back up what they say. I would have loved more but I am not exactly the average movie goer. The stories are one's I am familiar with having seen first hand what managed care leads to. My mother used to be a nurse. Insurance companies are what drove her away. There are Moore gimmicks but they are a welcomed relief. You need periods to laugh while watching this movie otherwise you would leave depressed. My fiancee teared up a few times while watching. Well worth it to see and start the dialog about changing our system.

License to Wed - This film stars Mandy Moore, Robin Williams and John Krasinski (The Office). It got lampooned by critics doing a little better at the box office than people expected (not great by any stretch but not a bomb). My fiancee and I enjoyed it. The audience we say it with laughed out loud a number of times. It is an amusing film with the simple message of communicate with your partner. Nothing deeper than that really save to set up the characters in silly situations. It isn't a deep movie but rather a light hearted movie with laughs. Sometimes in life that is what you need.

On to the blockbusters:

Transformers - Growing up I loved the Transformers. I watched the cartoons and had the toys even bought the comic books. This movie is a pure summer flick. It is just plain fun. There is humor and a little suspense thrown in but all in all eventually it comes down to stuff blowing up and robots knocking one another around. Very big thumbs up from me. My fiancee was not looking forward to seeing this but she dragged me to Pirates (which she was disappointed in) so our of fairness she say this with me. To her surprise, she enjoyed it as well. Not with the same glee as I did. It is a movie for the 10 year old kid in all of us.

Harry Potter and the Order of the Phoenix - I don't read the books so I know this franchise only through the films. The last movie was a little too patriarchal for my taste. Order of the Phoenix though was enjoyable. The shortest of all the Harry Potter movies which was good. Things moved along and who can resist a rebellion story against teachers overexerting their authority? Not me that is for sure. The overall plot of all the series starts to actually build. The movie has the task of having to end without completing the story but does so with a sense of closure. A thumbs up from me. My fiancee is a big Harry Potter fan (she reread book 6 to prepare for the final book coming out on Sat) and she really liked it.

Overall a good bunch of movies to enjoy. Other than Sicko, nothing deep or Oscar worthy (save for special effects and the like) but honest to gosh fun. Nothing wrong with that.

Tuesday, June 26, 2007

Review already in...

That paper I submitted a bit ago, the review is already in-very positive. The paper is not much. It describes a new method in more detail than what we have published in two research articles, including helpful suggestions. Still nice to get a nice review for the effort & to have it published. Now back to the experiments...

Saturday, June 23, 2007

Why an advisor with connections is good...

One good factor when deciding between two advisors (who are good fits for you personally) is what sort of connections they have. Not necessarily with regards to networking to get you a position after you finish (though that is not a bad thing per se though one must question it to a certain extent as it could keep the old boys network going) but rather when planning experiments. My current advisor (Wise, Kind, Rambling One, W.K. RO) knows practically everyone*. It is invaluable. You have a question, the advisor knows an expert who is friendly & directs you to said person.

My current projects require knowledge of bacteria for which I have not worked with before. For one, I need to know if an experiment has been done before. It is simple to do. Searches through the traditional places have not turned up anything. That doesn't mean it hasn't been done but published in a long forgotten journal. I informed W.K. RO, who immediately thinks of someone he/she knows who has expertise with the organism & contacts said person. It appears the experiment has not been done but the contact will do some more digging. As an added benefit the contact has already made suggestions on the project that will make my life easier. My other project requires fairly complex molecular genetics to develop the strains I need. W.K. RO has me contact the world's expert doing genetic manipulations with this bacteria after laying the groundwork for me. The exchange I have had with this expert has moved and developed the project in ways I hadn't even thought of before we started, setting me up in better position. The net effect should be better publications with less work. Life is too short to bang your head doing experiments that aren't going to be effective in answering the questions you are asking.

This is only a small taste of what help my PI is able to find for us in the lab. The reason my current advisor, W.K. RO, is able to do this is because he/she likes to collaborate and is nice, helping out other professors when she/he can. It is the Golden Rule in action. Not to mention W. K. RO is confident enough to say he/she doesn't now something and ask for help. They are simple concepts to understand & carry out but it amazes me how many faculty members burn bridges & can be egotistically pigheaded. Sometimes I wish a number of scientists would go back to Kindergarten because they missed some essentials from that grade.

Monday, June 18, 2007

Group meetings...

How do other people's labs handle group meetings?

We have two meetings a week. One is a research meeting in which one person presents his/her work in the last couple of months. The rest of us ask questions, make suggestions and have a dialog about what we are all doing. In theory people show their projects warts and all; not just what works. Some people have a hard time though showing the warts. My opinion is show it all. If you are having problems, someone else might be having similar ones and they can learn from what you did or did not do. Our meetings are friendly. People do challenge conclusions reached but do so in a non-confrontional manner. Heard in the past there were post-docs in the lab who were overly aggressive in group meetings & in lab in general which was not a productive research environment. They were asked to leave by the PI before I got there.

The other meeting is a journal club where someone presents a research article of interest which we then discuss. Usually this is less of a discussion than what is optimal because people don't read the papers ahead of time, most of the time due to the fact the person presenting doesn't pick an article until the night before or day of. Still it is nice to get a cross section of papers beyond my narrow subfield of a subfield.

In addition, once a month or so we have a concepts meeting. Someone prepares a presentation on some general topic and we discuss it. Many times it ends up being more of a lecture than anything else. Our PI brings in people from vary different backgrounds (microbiology, biochemistry, structural biology, computational biology, etc) so there is a lot of expertise to draw from which this format brings to the fore.

These meetings serve a secondary function of training us how to present. This can be tedious at times as our PI likes to discuss at times the details of what is wrong with a presentation. Some people never learn though and are constantly trying to write in yellow with a white background, not using spell-check, etc.

I know other labs do things differently. Not sure what way is the best. No matter the style the value in such meetings I find usually reflects on how the PI approaches the matter. Some are interested in actual learning & scientific discussions others are looking to see who will be their favorite. The latter leads to conflict and in my opinion unproductive meetings.

One paper down...

One paper has been submitted. Now another two need to be written-up after I finish an experiment I thought up last week that would be good to test for one of the two papers. After that a review to write. It never ends. Guess this is a good thing for my career but those rewards are down the line. Right now, I get eye strain & the frustration that is writer's bloc.

Friday, June 8, 2007

Chemical lab safety...

Dr. FreeRide brings up an interim final rule (what wonderful doublespeak by the way- it is interim but also final-- the interim is because the rule expires after three years) that will affect academic labs that has been brought up in Chemical & Engineering News.

From the article:
"To understand why academia was taken by surprise means backtracking a bit. Before promulgating the final rule, DHS, as required by law, issued an advanced notice of proposed rule-making (ANPR) on Dec. 28, 2006. The preamble and language of the proposed rule as well as the department's estimate of the number of facilities affected—about 40,000—led universities and colleges to assume that DHS did not intend for the rule's requirements to apply to them, and so they didn't comment on the ANPR.
That turned out to be a mistaken assumption, which academics only realized when DHS released a proposed list of "chemicals of interest" on April 9, a week after the final rule was issued. The list, published for public comment as Appendix A, contains 342 substances in "screening threshold quantities" that trigger reporting to DHS by facilities possessing them. This reporting is the first step of a multiple-step process to help the department determine which chemical facilities present what level of risk from terrorism.
The problem is that many of the listed chemicals are commonly found in academic labs, especially in the screening threshold quantities specified by DHS. More than 100 of the 342 substances, for example, have thresholds of any amount, which means that almost all universities and colleges—and most hospitals and environmental and clinical labs as well—would have to inventory their labs and complete an online form called a Top-Screen."

If this comes to pass, academic labs will have to be more "secure" including vetting teacher assistants and graduate researchers. In addition they will also have to do complete inventories of these chemicals. Who exactly is going to pay for this? Lets face it our advisors don't have time to do all their jobs well. There is only so much you can pile onto grad researchers and post-docs. Graduate students want to graduate. Post-docs to write papers to find jobs. Technicians and lab managers require money to pay their salaries. And lets face it universities that charge overhead are always looking to cut costs not take on new ones well unless it means expanding the size of the administration.

Proposed list find anything that is in your lab?

Tuesday, June 5, 2007

Ranking graduate programs...

Incoherently Scattered Ponderer has come up with a rubric to rank Physics programs based on the "percentage of PhDs from any particular program go on to become faculty members in R1 universities". ISPonderer carries out this analysis and finds for hires at top 50 research universities that "Top 10 universities contribute 59% of US PhD hires, those ranked 11-20 provide another 18%, the next ten ranked 21-30 provide 10%, and ALL of the remaining US universities contribute remaining 12% or so." The results may suggest pedigree matters.

In my mind this is a very flawed rubric. Who cares about hires at Top 50 research universities. There are so many more job opportunities than being a professor at a Top 50 institution. Maybe what this data is showing is the bias of the mentors as those universities. They push their students to think about just becoming professors at such places perhaps. Graduates therefore coming out of that environment are less likely to explore their options & devote more resources to getting hired as faculty members at an R1. Faculty members at those further down the list may be more open to letting their students explore options. Lets face it there are lots of options:

faculty-PhD granting university
faculty-master’s degree granting university
faculty-small liberal arts college
faculty-baccalaureate university/college
faculty-associate’s degree granting college
research scientist-academia
research scientist-industry
research scientist-government
research scientist-private institute
administrative-private institute
scientific writer
patent lawyer/agent
scientific advisor-government
scientific advisor-private institute
scientific advisor-industry

And I am sure there are tons more possibilities.

The rubric does not take this into account. It assumes that the point of getting a PhD in the sciences is to become a faculty member at a top research university. If you don't get one of those you are settling for a lesser position. That is absurd. A PhD is an academic degree. It is not a professional degree like an MD, JD, MBA, etc. Anyone selling the idea of getting a PhD to potential graduate students solely to become a faculty member at a Top 50 institution is selling a Pyramid Scheme & should be looked down upon in the same manner. I would strongly recommend avoiding professors like that. For graduate school, I was in a Top 10 institution in my field- many of the professors I am sad to say were like that. Mine was not. One of the reasons I choose that person. I was much happier, especially near the end of my graduate career than some of my peers. In fact a number of them would seek out my advisor for career advice because they could not talk about it with their advisors.

Be wary as well of professors who are open to other possibilities and encourage only certain students to explore (say based on gender).

Saturday, June 2, 2007

Movie round-up...

Sorry for the lack of posts. This past week was busier than I was suspecting. Work though hasn't consumed me totally though. I have seen plenty of movies in the last month or so. Here are my reviews:

Spider-Man 3- Fails to live up to the first two movies. It is sappy, corny and drags in many places. Basically it takes the worst aspects of the first two movies and expands them. First and foremost a super-hero movie should deliver action & fun. The heart and story has to fit into that rubric. That is the point after-all. SM3 it was like the action was tacked on. The story wasn't great to begin with. It is way too long.

Shrek The Third- The second of the third movie in a trilogy to come out in May. Funny. Not as laugh-out-loud funny as the first two though. Not a bad way to spend an afternoon, especially with the A/C they have in the movie theaters & the matinée prices.

Pirates of the Caribbean:At World's End- When would this end was what I was thinking half-way through this movie. Amusing bits here and there; fun action but a lot in between that just drags on and on. The back-crossing goes from amusing to tedious & trite very quickly. Like SM3, this movie is bloated, going for way too long.

Waitress- Excellent film. Go see this one. Keri Russel (of Felicity and All New MMC fame) is fantastic as Jenna, a waitress in a horrid/abusive marriage yearning to escape and start a new life but is unsure of how to do it. Andy Griffith is a hoot. It is uplifting, funny, and poignant. The rest of the cast are great. Adrienne Shelley wrote & directed as well as costarred. This was her last film. A critics favorite as well.

Knocked Up- Great flick. Laugh out loud funny. Judd Apatow (The 40 Year-Old Virgin) writes and directs-hitting another one out of the park. He has a skill at delving into raunch while still being smart & having a heart. Seth Rogan is great as Ben, a sweet foul-mouthed stoner who needs to grow up. Katherine Heigl is fantastic with wonderful comedic timing, especially in the little moments. The rest of the cast fits in perfectly. Joanna Kerns (Growing Pains) even makes an appearance. If you liked Apatow's Undeclared or Freaks & Geeks on TV and/or The 40 Year-Old Virgin, you will love this movie. The movie is doing very well at Rotten Tomatoes with critics (including the cream of the crop) and users alike.

Thursday, May 24, 2007

Writing, sun and some good reads...

The weather is great, lab work needs to get done as does a pluthera of writing, needless to say my blogging has taken a dip of late. Now to restart, I will stand on the greatness of others.

Mike the Made Biologist, discusses the original sin of the religious right-segragation. It feeds from one of the original sins of the United States-our treatment of African Americans. How many compromises since the nation's birth through modern times were on the backs of African Americans? There was the 3/5 compromise with the US Constitution, along with the fugitive slave provisions in the Constitution. There was the Compromise of 1820 and the Compromise of 1850. The Compromise of 1877 lead to the end of Reconstruction and basically turned the South over to segregationists right through the middle of the 20th century. The rise of the Civil Rights movements & calls for integration are what drove the Christian Right into action as Mike dicusses. Those are just the major compromises through the nation's first century of existence. Their effects still ripple through our nation. The politics of fear they spawned our what got the Bush Administration "elected" twice.

Changing topics, Incoherently Scattered Ponderer, ponders whether post-doc life is truly carefree.

Holly talks about actually walking at graduation where she got to listen to two presidents for the price of one. I skipped mine. Not exactly a pomp-circumstance type of person.

Kate ponders why we don't get science. Very interesting read and brings up questions then how to best reach people about science both in the short term and long term.

There are lots of great posts to check out over on the 4th Postdoc Carnival. Katie did a great job of putting it all together in addition to her usual excellent blogging.

Saturday, May 19, 2007

Must fight the procrastination...

I hate printing out papers, especially when I am reading them in order to cite them. It seems like such a waste of paper. So what is the green way of handling things? Download the PDF and read them in your favorite viewer on your computer screen. Which is all fine and dandy but if you are like me you then look up references in the paper. Of course this requires having your computer connected to the greater network that is out there. This means in turn, you can check your e-mail, catch-up on the sports scores, update my fantasy sports teams, read the news & blogs, check out some zany clip on youtube, download from itunes an episode of one of your favorite shows that you missed, etc. In other words, there are so many options that are more appealing than writing a review. Must fight them and write. A final draft is due on June 1st. I wish I could say that is it. In the cue are 2 research articles to write which I have been procrastinating on by thinking of new experiments, a review with another lab member and then getting my advisor to get out a larger review which has been ongoing project in the lab for the last couple years. How does the latter happen? Procrastination-which means it constantly needs to be updated with all the new info that is being published. Of course two years of doing that leads to a bloated review, so my task was to help cut so for the fat. Myself and another labmate have trimmed our parts to half the length they were before. Advisor was supposed to take the three page intro and turn it into two paragraphs. Still hasn't happened and slowly you can see the need to start adding again. So be warned-procrastinating over time can lead to more work!

Easier said than done though. My download is finished. TV on the laptop time.

Wednesday, May 16, 2007

Tenure, pipeline, teaching, oh my...

Rob Knop discusses his woes trying to get tenure at Vanderbilt. By all accounts, Rob is good at his job (teaches well, serves on committees, etc) except for getting grants. That will be his downfall. His point, if NSF is only funding 16-20% of all the grants submitted there are too many people trying to be faculty members (this is in astronomy). It is overly competitive, selecting people like him out. Some like Chad have pointed out that all the depressing news of tenure can be a negative, encouraging students not to pursue graduate studies. The key is going in with your eyes wide-open. The advice Chad got as an undergraduate was "the only reason to go to graduate school was in order to pursue a career in research-- which, it should be noted, is not identically equal to academia." (The latter is why it is important to choose an advisor in graduate school who is open to you exploring options besides being a faculty member at a research university).

Incoherently Scattered Ponderings and Open Reading Frame point to the fact that the bottleneck is not getting tenure per se but rather getting a tenure track position to begin with, the jump from being a post-doc. It is also why so many advisors can be such jerks. They figure if you leave, there is someone else who will be willing to jump through their hoops. Of course this selects for people in the sciences who are overly passionate about science relative to other facets of life. And when those people choose who goes to graduate school, they pick people like themselves-focussed on science and the cycle keeps going.

Of course what feeds this push for more post-docs/grad students than there will positions for? For faculty members to focus on getting grants and why it is so important for getting tenure? The dollars brought in from grants. Mike the Mad Biologist points this out in his skepticism of calls in Harvard for improved teaching leading to anything. Why? The selection is for money which comes from doing research and not from teaching.

From Mike:
"Overhead, also referred to as indirect costs, are a surcharge on the direct or actual costs* of the grant. More people on a grant and more research costs mean more 'indirects' for the institution. Typically, these indirects run 50-75% of direct costs."

"A certain amount of indirects is needed: all institutions have administrative and infrastructure costs (e.g., personnel, IT, utilities, and so on). But 50%-75% is exorbitant (and, incidentally, reduces the total number of awards federal agencies can give. Federal granting agencies subsidize higher education to the tune of billions of dollars every year***)."

In other words, we are funding higher education in the United States through science research grants. Universities get even more money from the government by charging PhD students tuition which is paid for by those federal grants. The tuition for PhD students in the humanities and social studies is usually waived (it was at GradU and it is waived at SnobU). SnobU by the way charges for internet access and email accounts in addition to the overhead so it takes in even more revenue. Universities are addicted to this grant money. It helps pay for administrative costs. It pays for non-revenue producing departments. It allows universities to grow their endowments which in turn makes them more prestigious attracting more students, allowing the university to be more selective and thus more prestigious. Faculty thus are under pressure therefore to get grants and keep getting them. The system puts a strong selection on keeping labor costs low (hence very few faculty positions relative to the number post-docs/graduate students) since so much grant money goes towards overhead but a lot of research is needed in order to get a grant. This sets up a situation that favors bringing more graduate students and post-docs into the system than their will be jobs for as faculty members. It also favors advisors trying to get every last drop out of those in their labs which is why so many push their post-docs and graduate students to work long hours.

The overabundance of PhD candidates & newly minted PhDs in turn creates an overly competitive environment between post-docs and graduate students, who for the most part are encouraged to shoot for being professors at research universities. It is why so many young scientists are so willing to put up with such horrible working conditions. The chances of getting a tenure track position are low. Getting a slightly better letter of rec. from your advisor becomes vital for your future.

The question is how do you break this cycle that feeds itself? Reducing overhead at this stage won't solve the problem because universities will just put greater pressure on advisors to get grants. More money will help but it can't just be in the shape of research grants. There has to be incentives for teaching well. For being good mentors. How do you put that into grants? It will also require graduate students and post-docs being more involved in how their departments are run, having a real voice and say. That is scary not just to administrators but also faculty.

Of course that would require these young scientists to organize. This seems unlikely as the competitive environment selects out those who would be most inclined towards this (Incoherent has a post on this centered around the number of scientists who played team sports as kids). Not to mention the current organizing seems to be centered around forming traditional employee unions. For graduate students especially, I think this would be a mistake. Being treated like employees is the problem. The fight has to be for fighting to maintain their status as students who demand quality teaching and mentorship. Who demand conditions that allow them to learn (which at this age group includes such things as child care). That of course requires revolution and effort but what choice do we really have? Are we really getting the best science for our dollars? What type of scientists are being churned out? Is this why scientists have trouble connecting to the general populace?

Thursday, May 10, 2007

Confidence, joining a lab and breaking a cycle...

Propter Doc had a visitor to her lab, a potential post-doc looking to join the lab. From the sound (or should I say read) of it, the visitor is clueless, a deer in the headlights. As Propter Doc discusses asking the right questions to the right people is key in figuring out if a lab is right for you. The other part of the equation is trusting yourself (i.e. having the confidence) not to go with the stellar name but rather what is the best place for you not just scientifically but also as a person. As PD puts it:
"And make damn sure before you turn up to an interview that you’ve removed from your little brain any nonsense about being ‘grateful for the opportunity to work with professor X/happy just to get a postdoc’. That’s just bullshit, and a pretty quick route to a very unhappy postdoc."

This of course is easier said than done. What if you have had a poor graduate school advisor who slowly eats away at your confidence? An advisor who makes your feel like you barely are getting by and are not working hard enough? How can said person really go into an interview for a post-doc position without feeling grateful for the opportunity? These are the ones who will get stuck in similar situations for their post-doctoral training.

In theory, thesis committees are supposed to protect against such advisors but in practice this doesn't happen nearly enough. There is no real incentive in the system for committee members to intervene other than being good people. In many respects, the system at research universities actually encourages them not to. If there is a problem, it takes effort to do something about it and time. Most PIs are exceptionally busy people. Most of them are not spending the time they should to be great mentors for their own students & post-docs and definitely the time to be good teachers in the classroom. Professors have to be writing grants, papers to get grants, dealing with university administrative duties along with duties for the general scientific community and giving talks. Add having a family on top of that and you do not have a situation where stepping up on behalf of a student in a bad but not horrible situation isn't easy to do.

How do you get around this? At the end of the day it will require money whether it is lessening the need to publish or perish, hiring faculty for different purposes, training PIs to be good mentors/teachers (& rewarding those that are). In addition though it will also require a change in the culture of science. Selecting for hard workers has to go. This encourages those most willing to endure long hours (not necessarily producing anything more with those extra hours) who don't have as much of a life outside of lab. Those are not people who will make good mentors for most people in graduate school. You would be amazed how many hours in lab are just wasted because the incentive is to "work hard" as measured by hours spent in lab.

Another change that must occur is that mentorship and teaching have to be greater components of getting tenure at research universities. They are places of higher learning. If said scientist doesn't want to teach & mentor then they shouldn't be professors at such places. Go to a research institute. Work at a company. Unfortunately, top tier research universities despite being school are all about churning out research to draw in grants. Their isn't a selection against poor mentors and teachers. You have enough of them, it isn't like graduate students really have a choice then on only joining labs with good PIs. The climate is to encourage students to join "hot" labs doing "exciting" science-the prestigious labs. Basically students get pushed into situations where they basically get used to generate data to keep these top labs going which brings money to the university.

Enough make it through the system, who are very grateful and drink the Kool-Aid to keep the cycle going. Graduate students and post-docs will have to stand up more and let it be known joining a lab has to be more than just the science.

More on choosing a lab:
Natural Scientist

Wednesday, May 9, 2007

Risks and reproductive rights...

Pharyngula links to a great blog, Well-Timed Period, that discusses issues surrounding reproductive health. One post in particular caught my attention; it is the one quoting from an article found in Contraceptive(Volume 73, Issue 5, Pages 437-439 (May 2006) that points out the relative risks associated with reproductive health as compared to one another and "everyday" type risks.

Here are some of the numbers:
Activity Risk of Death
(per year)

automobile accident 1 in 2900

In an airplane crash 1 in 250,000

Risk per year for women
(15-34) preventing 1 in 1,667,000 (non-smoker)
pregnancy using OCs 1 in 57,800 (smoker)

Risk per year for women
(35-44) preventing 1 in 33,300 (non-smoker)
pregnancy using OCs 1 in 5200(smoker)

Risk from pregnancy 1 in 8700

Risk from spontaneous abortion 1 in 142,900

Risk from induced abortion:
Mifepristone/misoprostol 1 in 110,000
Surgical 1 in 142,900
within first 8 weeks 1 in 1,000,000

In other words from the perspective of most woman, abortion and using oral contraceptives (OC) are safer options (especially if you don't smoke) than pregnancy or driving in a car. The pregnancy risk is not usually talked about by the anti-choice* crowd. There are risks associated with being pregnant and giving birth. Abortions are typically safer options for women than staying pregnant. Those lives saved don't really seem to enter into the discussions about abortion. What if those were men who were dying instead of women, would we care more?

Pregnancy is not easy. A woman is basically developing part of her body to become a separate being. Think how much energy we each expend to keep our bodies going let alone doing additional activities. Add on top of that, gestating part of yourself to grow to become another person that itself will need energy just to keep going, let alone grow. That is a lot of effort and that is just looking at things from a more macro view.

* I detest the pro-life naming of such groups. Many are not pro-life as they support the death penalty, wars, etc. Not to mention it is not like the rest of us are against life nor are we pro-abortion. We are though pro-choice. They want to limit the choices women have available to them.

Monday, May 7, 2007

A round-up...

Kate over on The Anterior Commissure has a blog piece on former Rep. Sherwood Boehlert's reaction to Mooney and Nisbet's pieces on framing science. Mooney promises a reaction as well.

The Ranger of the West discusses second homes near your undergrad institution.

Chad over on uncertain Principles asks, Why Physics?

The Propter Post-Doc touches upon Scottish politics (Independence v. nationalism), lab life and other topics including why House, MD.

Thursday, May 3, 2007

Sun through the weekend...

Can I say how great it is to finally have spring? It is amazing how my attitude changes. I wake up and I am chipper (ok more so than usual). I have energy at the end of the day when I go home. There is green around you. It is very nice. Lab during the winter can be a drag. The sun is barely risen (if at all) when I get into lab and has already set when I go home. The cold during the day doesn't encourage going out during lunch & when you do all you see are dormant trees. Basically for a person from a sunny state it is a nightmare. Spring though everything changes. It is almost like home. Of course it doesn't last long as summer with its humidity will show up soon, but I do enjoy the spring as long as I can.

Monday, April 30, 2007

More joys...

SnobU when it comes to Post-Docs, whether associates or fellows, does a poor job of integrating them. No orientations to welcome you, no sexual harassment training (how they legally survive this I have no idea), no information as I noted before. You are pretty much on your own. I knew enough to know that I should fill out a Federal W4, so I hunted down the form and filled it out, handing it to the human resources at SnobU. I did forget about the state W4 form (it has been awhile since I had a real job and there they gave me all the forms to fill out, had an orientation, etc) so my first full paycheck is a little bit smaller than I was expecting. I will get that money in a year but I rather have it now. There are credit cards to pay (including an engagement ring) and future debts I rather avoid thus the money does more good in my account today rather in a year.

Why didn't payroll at SnobU remind me when I handed in the Federal form? Come now, that would be giving information and making the life of a post-doc easier. That is not what SnobU is about. Unless they can bring in more money they really don't care. Everything is your responsibility. Talking with others, SnobU does seem particularly unique in this regard. Other places, there are orientations, they provide information which you then can use & is your responsibility to use. SnobU the responsibility extends to obtaining the knowledge. When joining a lab as a post-doc add what sort of institutional support is given to post-docs. Life is too short for spending time on such little things that are usually taken care of if you are in another position or at another university.

Friday, April 27, 2007

Framing the return...

Stephen wrote:

"I saw your comment on the framing post I wrote. You say that framing might be in dangerous hands when used by scientists, as scientists might "end up feeding into societal norms".

My comment is: if we all use framing in our daily life whenever we talk about our research to friends and family (unless your entire social sphere is made up of scientists), why would now be dangerous to frame when talking to the Anonimous Public?

We frame when we talk to somebody who does not agree with us; we frame when we want to make sure that somebody from the other side of the world understands what we mean...etc.

Look at the discussion started by Moran and PZ, about how successful rude suffragettes were: they are framing their approach to active atheism as something successful, successful because it has been show to be so, according to their interpretation, by history. Are they being dishonest, or dangerous, for that matter? No, they are just making a point. Maybe using a "frame" not everybody likes - it is a bit of a hyperbole - but making a valid point nevertheless."

The danger is how we frame. Nisbet advocates that scientists frame to get people to make up their minds "in the absence of knowledge, and importantly, to articulate an opinion." Dietram Scheufele when discussing ads for/against stem cells, which he highlights as good framing, reiterates the point "And they highlight a key aspect of successful communication. Neither proponents nor opponents of stem cell research build their arguments on scientific information. What they rely on are heuristics or cognitive shortcuts that will allow voters to make decisions without understanding the obvious complexities surrounding the issues. And it doesn't matter if these shortcuts are based on religious beliefs, celebrity, or personal hopes. Packaging matters ... regardless of which side of the issue you’re on." The point is to resonate with social identity of people. What helps create social identities? All the biases (sexism, racism, classism, etc). What does it take combat such biases that we all have? It takes time to think and to engage the actual facts.

Science in the United States is predominated by people like me, white males. We have blinders as we have privilege in our society. Look at this exchange last fall between Chad, Dr. Free Ride and Zuska (part II) regarding women in physics and the college level. Most of us men like to think of ourselves as the good guy and not part of the problem. The thing is if that was true thing would be a lot better. The evidence in the sciences, contrary to what Larry Summers might think, is that we do engage in a selection bias favoring men over women (read I, read II, read III).

Scientists are busy people. It is a working hypothesis as to why such sexism in science. They do not have the time to really sit down and look at the facts with regards to personnel decisions. What happens when you add engaging the public without focusing on the facts but trying persuade people? Aren't the odds favored towards playing to societal norms without even really realizing it?

Nisbet and Mooney are advocating this type of framing to get policy changed based on scientific data. It is not to promote science. They are very worried especially on issues of global warming. They don't think we have the time to live up to "the scientific or democratic ideal". It is about winning in the here and now. That puts a pressure to engage frames that are easy.

The easiest ones to engage tend to be the ones that fit into our societal norms.

What is the role of scientists in this debate? Should they be the ones engaging in framing issues based on shortcuts? Or should they be the ones injecting the facts? Framing is impossible to escape. It is harder to frame to communicate facts than to frame to play to someone's prejudices.

I would contend because of the dominance of white males and because they speak from a position of authority, that scientists should refrain from doing the former and focus more on the latter.

Moran and Myers are actively engaging in breaking down frames (and yes you frame to do that). It is different than what I have talked about or what Nisbet and Mooney are advocating. The are fighting societal norms. Nisbet and Mooney speak out against that as a strategy to win on issues in the here in now. That was the point of their WaPo piece by bringing up Dawkins and Myers.

To sum up my thoughts. The danger I see in scientists framing the way Nisbet and Mooney advocates is because so many scientists are from the dominant group in society. The pressure to win now selects for playing into culturally based biases which white males tend to have blinders to seeing. Overall I consider this to be negative for society and potentially harmful to science as it will keep science white male dominated in the US. Not to mention when the gotcha moment comes and the authority of scientists is undermined. Basically if the other side is not framing with facts, the easiest option is to pull a couple of choice facts that muddy the waters, through them out there and begin questioning the honesty of the other side.

Thursday, April 26, 2007

Hunting for benefits information...

SnobU is is not run to maximize the life of those doing research (see previous). I worked before going to graduate school. It was a salaried position at a research university. The benefits were nice. When I was hired, I got a slew of information such as what benefits options I would have. They also told me when the benefits meeting was. The key here is that this RU went out of their way to inform me of my choices and what needed to be done when. SnobU? Nope. You are told you to contact the benefits office in your letter of appointment within 30 days to discuss the benefits. That is it. It doesn't say you must contact the benefits in 30 days to get benefits just please do so and then once you do please inform your department's business office. No other information is sent your way. You have to actively pursue it. Of course when you call your benefits officer, the person is not always available which leads to a string of phone tag if you are lucky or waiting for someone to call you bac. On top of that, the benefits office is closed half a day/week. It is more trouble than it should be. I am sure it is cheaper for SnobU to run things this way but really when starting a post-doc, should I have to be going through all of this? How hard is it really to send me a packet with information? If the other RU can do it, why can't SnobU? Why must I hunt?

Wednesday, April 25, 2007

A round-up...

Waiting on cells, what fun let me tell you.

Here are some great reads to check out:

Tara at Aetiology has:
A discussion on the fact there is not a link between having an abortion and getting breast cancer and breast milk sharing

On Panda's Thumb Nick Matzke continues his critique his critique of the flagellum evolution paper that came out in PNAS. It is like an online journal club.

Over on Uncertain Principles, Chad wonders When Honor Codes Go Bad.

ScienceWoman has exciting & well earned/deserved news.

FemaleScienceProfessor debates Dr.DeMentor on whether to be an administrator or not.

Incoherent Pondering discusses the fact we in the science are kinda like monks.

Ranger of the West brings up the fact our government farming policies are actually encouraging us to eat poorly.

Kate at Anterior Commissure talks about her experiences teaching and what she has learned from her evaluations.

PhilipJ over at Biocurious asks, are there too many scientists?

Jooyla at N@ked Under My Lab Coat ponders the hierarchy of toilets and how it applies to our sexist society.

Gas prices...

The SF Chronicle has a piece on raising the gas tax. The logic being people need to be encouraged to drive more fuel efficient vehicles and cut back on their driving. The net effect being that we as a society would use less fuel decreasing the amount of greenhouse gases we emit and decreasing the amount of pollution in the air. The only problem is that is a regressive tax. Those with the largest disposable incomes will feel the effects the least. The working class would feel the pinch the greatest as they need to drive to work and don't have large disposable incomes.

Mass transit in the US just isn't at the level to allow a large segment of our population to use alternative means to get to work. That infrastructure needs to be built. The problem though is that most transit projects are paid for by gas taxes. My solution? Increase the "guzzler tax" and include SUVs & light trucks. The cost of gas guzzlers on society is shared by everyone while those who buy such vehicles get the benefits. Shift these costs from the society as a whole onto those who are getting the most benefit. The fuel standards for the tax should change over time to put more and more pressure to have fuel efficient cars on the market. Tax the revenues that the auto companies make off of these fuel inefficient cars. Put this revenue into improving mass transit options & credits for buying super-efficient cars. States should also adopt a "guzzler tax" when it comes to DMV/registration fees. Gas guzzlers should cost more to own. Put this money also into improving mass transit. End all subsidies to the oil companies, once again putting the money instead into improving mass transit and in addition funding research for alternative technologies.

Increasing the gas tax then should be phased in to encourage people to use the options available to them. The later phase in once there are options for people to use, will reduce the regressive nature of the tax (though not completely). The benefits are there for us to gain from reducing the amount of fuel burned by our automobiles (Societal Costs of Gasoline; updated for Climate Change) the question is who do we ask to carry the burden?

Tuesday, April 24, 2007


The latest What's Up Post-Doc is up. Check it out, some great reads. And thanks for submitting me. Very kind.

The latest Scientiae carnival has been up for over a week. Once again great reads. Check them out.

Saturday, April 21, 2007

Great program for Mac users...

Alexander Griekspoor and Tom Groothuis ( have written a wonderful program for Mac users that lets them manage their collection of science papers called Papers. It is a great tool allowing one to search pubmed, grab citations, organize them into useful smart groups, download & save the PDF in organized manner, export the citation to your favorite reference program, and to search the downloaded PDFs all in one application. It is very handy. It is still in the public preview stage but I have found it to be very useful & easy to use, well worth the small fee to buy. Have no fear though buying now enables you to use both the public preview and the 1.x versions of the software. The duo are the ones behind 4Peaks, a great DNA sequence viewer, EnzymeX, a wonderful DNA sequence analysis/editing tool, Lab Assistant, an electronic lab organizer (sticky, timer, lab journal all in one), and IRNAI, oligonucleotide design program, all of which are free. I use the first two programs frequently in lab. I can't comment on Lab Assistant and IRNAI though they appear to be solid programs.

Update- Papers is now available as version 1.0. Downloaded it and will be giving it a test drive this week.

The Science Sampler, Daily Transcript and Thoughts from Kansas also have discussions about PDF organizing including using iTunes.

Thursday, April 19, 2007

Can't it be spring already...

I just want it to be spring. I am not a native of New England. Winter dragging into spring is foreign to me. My body hates it. Migraines flare up, eyes hurt and I just feel blah. At least this weekend it will warm up and be sunny (or so they say). Hopefully my energy and productivity will go up as well. So much to write (three reviews (luckily a co-auther on each) and two research articles) to close out my thesis work. As for my Post-Doc work planning for the major one which takes me from the biochemistry realm to the land of playing with cells which will be fun but risky. The two side projects are biochemistry but should get me on a couple of papers. Hedging your bets in science is a good way to do things. Out of my grad school work I will have 6 research articles, all based on side projects that together eventually became my thesis after the trials and tribulations for two and a half years on what had been my main project (developing an in vivo system was more challenging than expected and by the time we got it going the company whose technology we were going to use for free was burning way too much money to engage in anything academic, such is life).

Saturday, April 14, 2007

What us males should read...

Before pulling a Kos or an Imus, us males really need to read this post on Pandagon by Chris Clarke and internalize it. Many of us men at times speak without thinking at times and other times when we should speak, we say nothing. It is what keeps the cycles of sexism going in society which opress our fellow humans and limit us all.

Friday, April 13, 2007

My little voice in support...

I would like to add my voice of support of Bitch PhD and Pharyngula for calling Markos Moulitsas Zuniga out on his comments regarding the unacceptable threats and harassment Kathy Sierra has received. Kos writes about his opposition to an online code of conduct which is fine and dandy but then he dismisses the experience Kathy Sierra has gone through. Basically what Kos is saying if you can't handle the heat, don't voice your opinion. The level of harassment/threats Sierra was subjected is not acceptable. Kos in theory is an online leader. He should be setting an example & calling out such blatant sexist behavior not blaming the victim.

Choosing labs- a series to read

A Natural Scientist has a great series about joining a lab which is a must read for those thinking of joining a lab; it is far more detailed than my one post on the matter, more eloquent and thus more useful. (part I, part II). It also includes a first hand account of what happens when you choose a lab that is not a good fit which mirrors what some of my friends in graduate school experienced. I have also heard of horrifying post-doc experiences including a post-doc that switched from one such lab into the one I am in. The stories that post-doc tells are still shocking to hear.

Updated: part III.