... ponderings of a fool

How is that fair or democratic?

2008-03-14T06:17:00.003-05:00

Markos Moulitasas (kos of the Daily Kos) has been pushing that the Democrats divide the delegates from Florida and Michigan 50/50 (half for Senator Clinton and half for Senator Obama) to solve the problem of not seating the delegates from the two states at the Democratic Convention later this year. You see the Democratic primaries in those two states were held early, against the rules of the Democratic National Committee. The same thing happened on the Republican side. The GOP decided that the punishment will be that the delegate count from each state will be halved. In other words there was a punishment for not following the rules of the party but the votes would count and the Republicans in those states would get a say in who was the nominee from their party for president of the United States.

What did the DNC decide? Well those brilliant Democrats decided to punish those states by not counting them. The major candidates went along. Senator Obama did not even end up on the ballot in Michigan because of this. He was on the Florida ballot. Senator Clinton was on both. She ended up winning both primaries (they were still held). The DNC was betting the nominee would have been secured by now, so it wouldn't matter. Boy were they wrong. Instead we have a situation in which Obama has a slight lead over Clinton in pledged delegates (those won through caucuses and primaries). Neither one may get enough pledged delegates to win the nomination. In that case, superdelegates will decide. These superdelegates are party officials, party elders, and those Democrats who were elected to high governmental offices. That doesn't exactly come across as being well very democratic, especially when the voters in MI and FL will not get a say. It will be a brokered election where back room deals come into play. While that made for fun viewing on West Wing, it will likely not play well in the real world.

This brings us back to Kos. You see he is for Obama. Clinton needs the delegates from MI and FL in order to have a shot at winning (on top of big wins in PA and Puerto Rico). A revote along with the votes in PA and Puerto Rico may mean she will have more "popular votes" than Obama by the time of the convention while Obama will have a slight lead in delegates. This would be shades of the 2000 presidential convention. Gore won the "popular vote" while Bush ended up getting enough electors. Him getting enough electors of course being decided by the Supreme Court. For the Democrats it will be the Superdelegates playing the role of the Supreme Court. Obama camp would be in the uncomfortable position of advocating for a similar scenario that put Bush into office for him to be the nominee. They obviously do not want this but at the same time they don't want to offend the voters in Michigan and Florida, key swing states in the general election. Plus if they don't count and Clinton can convince enough superdelegates that she would have won if Michigan and Florida counted, she can win the nomination. By playing that angle, Clinton comes across as supporting the will of all the people. Obama would come across as attempting to suppress voters.

The solution some are offering and Kos is pushing? Split it 50/50. The states get a "say" and Obama gets his pledged delegates. All is fine in the world. Of course all is not fine since there is a good chance Clinton could win both primaries. In other words the voters would not get a say. It would be sham and the nominee will be selected by the superdelegates, some of whom were part of the decision to strip the two states of their delegates to the convention. Of course this is a party that allows people to vote twice in Texas (they hold a primary and then a caucus, you have to vote in the former to participate in the latter needless to say certain demographics get underrepresented in the latter since they don't have the time). I am no fan of Clinton. Not voting for her in the general nor would I vote for Obama (the electoral college means my vote doesn't count so I say if that is the case I am going to stick to my principles). The Kos method is all about winning over substance, over democracy. This is personally what I think is wrong about American politics. It is all about winning the next election rather than you know actual leading through a democratic process. Not to mention it treats the people of MI and FL like they are idiots, it is patronizing them. Do we really need more of that in American politics?

Updated:
Obama favors the 50/50 split. Clinton camp not so much. No real surprise. And yes, if positions were reversed, I think Clinton would be pushing a 50/50 split. Principles, what are those?

Finally...

2008-01-25T06:53:00.000-05:00

Well as I mentioned awhile back, I have been busy writing away. Both the wet-lab work and the computer-based results were submitted together to the Journal of Cool Stuff . This was my first time submitting to J. of Cool Stuff. My advisor hadn't submitted there in awhile. The review on the computational work took 6 weeks. Minor revisions, mostly highlighting things for the reviewers that were not as obvious as we originally had thought. Easy fix. It took 8 weeks to hear on the wet lab work. Accepted pending minor revisions which included additional experiments along with curtailing the discussion or doing even more experiments. I took a week did the easy additional experiments (all yielding the negative results I expected with tons of caveats that make it hard to say anything conclusive about them, hence I did not do them in the first place, but we included all of that in the revised paper), and then we curtailed the discussion. The further potential experiments I am now doing and will turn into a short article, which in the end I guess puts me ahead of the game. I guess a thank you to the reviewer is in order.

The work I did for collaborators currently is sitting in their hands as they write their part. Glad there was a delay since in the meantime I wrote a review with another post-doc in the lab for Building Blocks Journal which was reviewed & accepted within the span of two weeks for the holidays. Our lab has submitted research articles to Building Blocks Journal they are also turned around in the same amount of time. We already sent back the proofs. Still waiting on the proofs for the articles for Journal of Cool Stuff. The reviews for BBJ are very complete. Their editors actually push the reviewers to you know actually review in a timely fashion. Wish other journals did the same thing. Nothing worse than waiting, wondering if you are going to have to drop what you are doing to do additional experiments to satisfy a reviewer. Better to get it done sooner rather than latter. You have to be able to move on, move forward, so much better for peace of mind.

And now what? Well, it is work with a post-doc in the lab pushing for a paper, work on the further experiments discussed above for another and then also work on a third project that hopefully will turn out a paper before the year is out. Productive yes, which is good but boy can writing be draining.

A day to remember what we forget as a nation...

2008-01-21T07:02:00.000-05:00

Today in the US is Dr. Martin Luther King, Jr. Day. It is a day in theory we are to remember the work of Dr. King and by extension the Civil Rights Movement in this nation. Usually I am afraid to say we gloss over it looking at through safe feel good frames, of peace and brotherhood. We must force ourselves to remember. There is much still to be done. Equality is still a dream we are striving for.

I offer these reminders on this day of the work still to be done, still to be thought about and discussed. What we must remember.

The March on Washington in 1963 (The one in which Dr. King gave his "I have a dream" speech) was the March on Washington for Jobs and Freedom. What were they advocating for?

Comprehensive and effective civil rights legislation from the present Congress — without compromise or fillibuster — to guarantee all Americans:
Access to all public accommodations
Decent housing
Adequate and integrated education
The right to vote
Withholding of Federal funds from all programs in which discrimination exists.

Desegregation of all school districts in 1963.

Enforcement of the Fourteenth Amendment — reducing Congressional representation of states where citizens are disfranchised.

A new Executive Order banning discrimination in all housing supported by federal funds.

Authority for the Attorney General to institute injunctive suits when any Constitutional right is violated.

A massive federal program to train and place all unemployed workers — Negro and white — on meaningful and dignified jobs at decent wages.

A national minimum wage act that will give all Americans a decent standard of living. (Government surveys show that anything less than $2.00 an hour fails to do this.)
[The minimum wage at the time of the March is $1.15/hour.]

A broadened Fair Labor Standards Act to include all areas of employment which are presently excluded.

A federal Fair Employment Practices Act barring discrimination by federal, state, and municipal governments, and by employers, contractors, employment agencies, and trade unions.

Dr King on the Vietnam War:
"A true revolution of values will soon look uneasily on the glaring contrast of poverty and wealth. With righteous indignation, it will look across the seas and see individual capitalists of the West investing huge sums of money in Asia, Africa and South America, only to take the profits out with no concern for the social betterment of the countries, and say: "This is not just.""

Dr. King on capitalism:
"You can't talk about solving the economic problem of the Negro without talking about billions of dollars. You can't talk about ending the slums without first saying profit must be taken out of slums. You're really tampering and getting on dangerous ground because you are messing with folk then. You are messing with captains of industry… Now this means that we are treading in difficult water, because it really means that we are saying that something is wrong… with capitalism… There must be a better distribution of wealth and maybe America must move toward a democratic socialism."

The latter sentiments lead Dr. King to begin to push for what he thought of as the 2nd phase of the Civil Rights Movement, dealing with poverty across the board (the first phase being taking on the challenge of segregation) with the Poor People's Campaign where he was going to champion for an economic bill of rights. He was assassinated in Memphis, TN before he had to chance to really push the campaign. Dr. King was in Memphis to support striking Black sanitation workers.

We must remember. We have a long ways to go. We have a history of only going so far to deal with the inequalities in our society. We gave up on Reconstruction after the Civil War, turning the South over to the segregationists, rewriting our history to look poorly upon Reconstruction (Gone with the Wind anyone). We only ended segregation in name only. We failed to do the hard work of actual integration. Giving instead into fears of "other" breeding the modern Republican Party and with it the presidency of George W. Bush.

BCS Nightmare II...

2007-12-29T09:54:00.000-05:00

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!

Back...

2007-12-26T19:01:00.000-05:00

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.

Rooting interests or the BCS nightmare scenario...

2007-11-24T08:04:00.000-05:00

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.

Sociobiology, evolutionary psychology and Chimps. Oh my!

2007-11-19T07:43:00.000-05:00

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).

Remember in '08, Vote Colbert!

2007-11-01T16:26:00.000-05:00

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!

Absence...

2007-10-24T17:26:00.001-05:00

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!

Give a little and help improve science education...

2007-10-11T17:17:00.000-05:00

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!

GradU asking for money...

2007-09-29T22:57:00.001-05:00

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.

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

2007-09-24T18:58:00.000-05:00

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.

September carnival...

2007-09-20T09:45:00.001-05:00

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

Cheaters and casting doubt...

2007-09-15T07:06:00.000-05:00

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.

On tenure again...

2007-09-10T13:40:00.000-05:00

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.

PAUP Help...

2007-09-09T18:56:00.000-05:00

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

2007-09-09T09:07:00.001-05:00

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

Blogger day (a day late)...

2007-09-02T16:36:00.000-05:00

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.

Why?

2007-08-29T15:20:00.000-05:00

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.

Posts to read...

2007-08-28T12:30:00.000-05:00

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
Pharyngula
Sandwalk I Sandwalk II
Genomicron

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...

2007-08-28T12:14:00.000-05:00

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!

Oh what great news...

2007-08-23T12:02:00.001-05:00

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?

The heat, oh the heat...

2007-08-20T05:54:00.000-05:00

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.

Ummm anyone see something wrong with this?

2007-07-20T18:02:00.001-05:00

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...

2007-07-20T07:36:00.000-05:00

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.

Review already in...

2007-06-26T08:57:00.001-05:00

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...

Why an advisor with connections is good...

2007-06-23T18:45:00.000-05:00

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.

Group meetings...

2007-06-18T07:15:00.000-05:00

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...

2007-06-18T07:11:00.001-05:00

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.

Chemical lab safety...

2007-06-08T05:50:00.000-05:00

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?

Ranking graduate programs...

2007-06-05T05:44:00.000-05:00

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-academia
administrative-government
administrative-industry
administrative-private institute
consultant
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).

Movie round-up...

2007-06-02T09:06:00.000-05:00

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.

Writing, sun and some good reads...

2007-05-24T06:03:00.000-05:00

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.

Must fight the procrastination...

2007-05-19T08:56:00.000-05:00

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.

Tenure, pipeline, teaching, oh my...

2007-05-16T05:51:00.000-05:00

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?

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

2007-05-10T05:35:00.000-05:00

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:
Me
Natural Scientist

Risks and reproductive rights...

2007-05-09T07:21:00.000-05:00

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.

A round-up...

2007-05-07T07:00:00.000-05:00

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.

Sun through the weekend...

2007-05-03T06:06:00.000-05:00

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.

More joys...

2007-04-30T06:56:00.000-05:00

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.

Framing the return...

2007-04-27T05:50:00.000-05:00

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.

Hunting for benefits information...

2007-04-26T08:43:00.000-05:00

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?

A round-up...

2007-04-25T14:16:00.000-05:00

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...

2007-04-25T09:31:00.000-05:00

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?

Carnivals...

2007-04-24T10:01:00.000-05:00

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.

Great program for Mac users...

2007-04-21T06:27:00.000-05:00

Alexander Griekspoor and Tom Groothuis (mekentosj.com) 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.

Can't it be spring already...

2007-04-19T06:11:00.000-05:00

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).

What us males should read...

2007-04-14T07:32:00.000-05:00

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.

My little voice in support...

2007-04-13T11:53:00.000-05:00

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

2007-04-13T11:32:00.000-05:00

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.

Am I missing something? Or am I just suppossed to accept the world as it is?

2007-04-12T11:05:00.000-05:00

The more and more I read from the neo-framers, the more and more I am concerned. Am I missing something? Knowing your audience and communicating ideas/concepts are something I think all of us can get behind. Framing though, at least how they are portraying it, seems to be a different beast.

I already commented on Nisbet's comment regarding framing as a means to have people make up their minds in the absence of knowledge. On Nisbet's blog he refers people to Dietram Scheufele blog articles on framing science. I decided to take a look. The Oct. 23, 2006 piece on Framing Wars Religion vs. Science caught my attention. With regards to the stem cell ads & the frames used he writes:
"And the strategy of recasting opponents of expanded stem cell funding as anti-science and anti-life may very well work on November 7. But more importantly, these attempts to establish one frame over another are good indicators of what we can expect for future debates about emerging technologies, such as nanotechnology.

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."

To me it is dangerous to base decisions on such shortcuts. As noted in the Handelsman et al. piece in Science in 2005 on More Women in Science, Richard F. Martell demonstrated that "only when subjects were able to carefully allocate all of their attentional resources did sex bias in work performance ratings abate". In other words, the work suggests unconscious bias requires thought to overcome. There aren't shortcuts when fitting these biases. It requires time to think and evaluate the objective facts. The subjective leaves people open to making choices based on these biases. What Nisbet, Mooney and Scheufele are encouraging is exactly that, decision based not on the facts but the subjective biases lenses we all have.

I have not yet seen them address this concern. What limits will be in place to insure in the quest to win public opinion on issues such as stem cells, global warming, etc. that they don't frame to tap into these biases? What selection will keep that from happening?

In a democracy how you come to a decision has to matter by definition. The subjective is a very dangerous place to be. Fear can overtake reason very quickly.

Am I being overly concerned about what is being suggested? Or have things gotten that bad that scientists must act in this manner to prevent the "other side" from "winning"?

Framing science (Part II)-A revolution will be needed...

2007-04-11T07:19:00.000-05:00

The more I read about the "framing of science" of Mooney and Nisbet the more I am skeptical of what they are trying to accomplish and that they are naive about the enterprise of science itself.

Part of the push Mooney and Nisbet are making for frames is that they want to tackle issues now, which science education won't affect in the next election cycle.
"Science education is critical, but it's also a long-term approach. It doesn't help us deal with the highly politicized hot-button issues that are playing out over the course of an election cycle--like embryonic stem cell research, or like global warming. On these issues, the frames game has already begun, and scientists are way behind. We simply can't wait for a better educated generation to come along and deal with these subjects in a wiser way. It will be too late."

In response to the idea that scientists are already busy:
"Matt and I never meant to suggest that every last scientist has to become a top notch framer. Rather, we want scientific societies, institutions, and universities to rearrange their priorities and step up to the plate on this. That means training a generation of better science communicators (although many scientists will assuredly opt out of the "framing" curriculum). It also means launching communication initiatives--such as advertising--targeted at specific publics, and using the right frames to reach them.

The average bench scientist can happily duck all of this--there can be a division of labor--but for the scientific community as a whole, it's essential."

Ok so Chris and Mike wants to start doing framing in the here and now but want to have major institutions to change how they operate, to spend resources on framing. Ummm, how in the world are you going to make that happen? Societies are run by working scientists. They are busy people. Not to mention, those who probably would be the best communicators of science are usually those that are selected out of science (i.e. those that are not willing to endure the process of getting a PhD, trying to be a faculty member). Universities? Many of them are being run like corporations. Why would they spend money to frame science when they will not see the benefits in the short term? I mean if they were altruistic wouldn't research universities be spending more effort and money to improve undergrad science education? Base tenure on more than research and bringing in grants (on say teaching perhaps)?

There is also the fact many advisors do not exactly look kindly on grad student/post-docs who spend time away from bench work doing things like teaching, learning to teach, to communicate, etc. Those students are not rewarded in the current system. Of those students who want to go on to teach, to go into policy, into science writing are actively shun by many advisors. How do Chris and Mike plan to change that? Without more of those type coming out of graduate school, who is going to frame? The ones who tend to be better at communicating and teaching already handle more than their fair share of duties and labor at most universities. You can't expect them to do more and have families, to have lives outside of science. Having families and lives is exactly the type of grounding that is needed for scientists to frame things correctly.

In order to accomplish what Chris and Mike set out to accomplish, a revolution is necessary. They are not going to be able to "win" today unless they do that. In addition to widening space in the sciences for those who have a passion to teach and communicate is also the need to add diversity. I mean really how are you going to reach out to minorities and women when science is still dominated by white men? Framing just isn't about the message but also the messenger.

Nisbet: "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."

By playing into biases and ignorance to win a battle today means Mooney and Nisbet are actually making harder to attract the diversity needed in the science to effectively communicate. Citizens making up their minds without knowledge is exactly what holds back minorities and women in our society. That should be fought tooth and nail.

Revolutions start small. People like Mooney and Nisbet need to make space for those currently in the system to do more science framing/communicating to the general populace but in addition make space for those trying to change graduate education, universities. They need to frame things to catalyze the necessary revolution to turn out the type of people who can fill the role of science communicators at societies and universities. The framing though can not be about winning at the expense of the future of science.

Framing science (Part I)...

2007-04-10T18:36:00.000-05:00

Dr. Matthew Nisbet and Chris Mooney wrote a piece on Framing Science that has appeared in the latest issue of Science. Nisbet is a professor of communications at American University while Mooney is a science writer. Its message is that scientists need to frame their work. How?
"Frames organize central ideas, defining a controversy to resonate with core values and assumptions. Frames pare down complex issues by giving some aspects greater emphasis. They allow citizens to rapidly identify why an issue matters, who might be responsible, and what should be done."

One of their examples is Evangelical leaders framing "climate change as a matter of religious morality". They really don't go further in the piece. In fact that is my major criticism of the entire article. It is very general and fluff. The take away I got from it was that scientists need to know their audiences and not drown people with technical details. Ok, not exactly revolutionary. It is teaching or communication 101. Of course what are the technical details that should be left out? No answer is given. How should scientists be going about framing?

Nisbet argues on his blog in response to Dr. Myers question what about those pushing to break the frames:
"investments in formal science education and traditional science media remain important as long term strategies, since these initiatives will hopefully sponsor generational gains in citizen knowledge (and maybe actually change world views.) But PZ's hoped for revolution won't happen over night. Indeed, in the contentious policy debates that take place over the next election cycle or decade, scientists must learn to focus on "framing" their messages in ways that resonate with Americans' existing world views.

More than 80% of Americans believe in God and going to church remains the most popular of American volunteer activities. As a result, with many members of the public, communicating on issues like climate change or evolution means developing messages that resonate with, or at least complement, their religious identities."

In other words it is don't be a revolutionary, be a liberal. I can agree with being incremental in the short-term with longer-term goals. Revolution is rare and minor improvements now are still improvements; the threat of one though tends to push incremental changes to occur. The problem is when you start going for short term "wins" makes it harder for true change in society which is what I am afraid to say is what Nisbet is advocating for:

"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."

In my mind playing into "how things work in society" is to the detriment of science. As a scientist why do I want to enable people not thinking? Why would I want to be directly party to undermining my life's work? Science is a process to understand how the universe works that asks us not to accept the word of an authority figure but to question authority. Given the current Bush administration, haven't we learned that not questioning authority is dangerous? Shouldn't we be discouraging people from making up "their minds in the absence of knowledge"?

Values...

2007-04-09T07:05:00.000-05:00

Mike the Mad Biologists raises an interesting contradiction in wages:

The chairman (currently Dr. Ben S. Bernanke) of the Federal Reserve makes $186,000/year while according to preliminary numbers from The Corporate Library as reported by the AFL-CIO, the average CEO of an S&P 500 company makes in compensation about $14.78 million/year. Interesting that the salary controlled by tax dollars is so deflated while those dictated by boards of directors is so inflated.

In 2005, if the minimum wage as of 1990 had gone up in value as much as CEO wages over the same period of time, it would have been $22.61 (adjusted for inflation). The average worker would have made $108,138/year instead of $28,315.

CEO compensation is dictated by the board of directors. Boards typically include many CEOs or former CEOs. If not CEOs, they typically are other executives or political figures. Sometimes academics make it as well. The Board of Directors of Apple are:
Bill Campbell, Chariman & former CEO of Intuit
Millard Drexler, Chairman & CEO of J. Crew
Albert Gore Jr, Former Senator/VP of the USA
Steve Jobs, CEO of Apple
Arthur D. Levinson, PhD, Chairman & CEO of Genetech
Dr. Eric Schmidt, CEO Google
Jerry York, Chairman, President & CEO of Harwinton Capital

The board of Time Warner is not much different. Nor Wal-Mart. Nor Coca-Cola.

And what does a post-doc start at? $37,000. With 7 years of experience? $51,036. (NRSA is usually used as the guideline for post-doctoral salaries in the basic biomedical sciences).

Is this really an efficient use of resources? People like to complain about governmental bureaucracy but what about the bureaucracy in the corporate world that is inflicted upon us? Ever try to get ahold of someone at the telephone company. Cable? And if they screw up on your bill, forget about it. Mind numbing waste of time and energy and resources. We pay more for less while those at the top make more and more. What a wonderful world.

A good start...

2007-04-05T12:26:00.000-05:00

Princeton is taking a good step in being more family friendly for graduate students. What is being offered according to Insider Higher Education:

"Three months of paid maternity leave, along with extensions of academic deadlines and fellowships, so leave time does not count against any limits on time to receive financial support or finish degrees.

Child care support of up to $5,000 a year per child (for up to two children).

Additional funds to pay for child care — either at home or on site — when graduate students need to travel for academic conferences or other events related to degree programs.

Additional funds to pay for back-up child care when regular child care is not available.

Mortgage assistance, which can be used anywhere in the country, that would reduce both points and closing costs for graduate students purchasing real estate."

It is a good first step. One of the negatives if you look closer on the Princeton site is that it focuses with regards to time off on birth mothers or primary caregivers. The way it is worded a father could take time off instead of the mother, if he becomes the primary caregiver (and this is all assuming a traditional heterosexual relationship; what of those who adopt? homosexual couples?). Ideally, they should have time off for both parents with the expectation that they both actually use it. Right now the burden still is primarily on the woman when it comes to family matters, which means the system favors men staying in academia (especially in the sciences) regardless of the benefits. If you really want to change things that has to be addressed. What also needs to be addressed is the attitude of advisors. If an advisor looks down on time off and gives a student a hard time, what recourse can students take? Are the universities going to be proactive and educate their faculty to respect students taking time-off to be with family? In order for this effort to really be successful those have to be addressed, especially when you have many faculty who have a "back in my day" mentality when it comes to families and maintain the nonsense of "needing to work 80 hours/week". By the way, does anyone actually have evidence for the latter?

Reviewing...

2007-04-03T05:44:00.000-05:00

Somehow in the last week or so I have reviewed three papers on totally different subjects. Two were in areas which I know the literature, techniques, etc. The third, I know generally of the field (my advisor knows as much as I do). The latter paper was much harder to review since I am not up on the field and there are only so many papers I can read to review one paper. Experimental design was where I focussed my efforts on that paper, making sure the proper controls were done, etc. Hopefully another reviewer works in that field and was able to comment more on the discussion.

The first two papers I had to sit back a few times from reviewing and ask other people if I was being fair in what I was asking the authors to do since I know the subfields pretty well & can think of plenty of experiments on the subjects that would strengthen the papers. I try and be positive in my reviews, trying to get any critiques to come across as making the paper even better. It is not an easy task when controls are missing. Nobody likes getting a review back and having to do more experiments. I know I don't. Once I have submitted a paper, the most I want to do is revise what is written and when it comes to bench work I want to move on to new things. Controls though must be done. Who wants to be the reviewer of a paper that has to be retracted?

At least at this stage in my career my advisor goes over the paper and my review, so it isn't really on my shoulders yet. I am still training, still learning.

One things I must say, report errors. Don't try to tell me a 10 to 20% increase in activity is significant without them especially if other papers report errors using the same assay anywhere from +/- 10 to 40%. Also, do a literature search prior to submitting especially if you make statements of the nature it has only been done once or not at all. If I can do the search as a reviewer then you can as an author. Basically, don't try to oversell your paper.

Roundup...

2007-03-29T08:04:00.000-05:00

Busy working away. A few links.

Aetiology brings up the latest and greatest that has come out in the microbiology/public health realm and discusses TB anywhere is TV everywhere.

Science Woman opens up her in-box, including advice for those interested in getting a PhD in the sciences.

The Science Professor discusses sexism in blatant form originating from a science department in Europe, equal opportunity invisibility, turnabout (or why being sexist just might bite you in the rear someday), and SpaceWars.

Uncertain Principles brings up class and admissions to college, whether merit scholarships are a threat or menace and when grad students snap (never, ever let Fox hear about this).

Dear lab...

2007-03-27T13:55:00.000-05:00

Dear Lab,

Ok Drs and Drs. to be, you are bright people or so I am told.

Why, oh why, can't you place empty bottles, boxes, etc. out in the hallway like you have been told? Why do you return them to where you found them making your lab-mates think we have more of reagent X than we actually have? Is it really that much harder to place them outside the lab? Even more perplexing though, why when said bottles, boxes, etc. are still full do you not put them back? It makes no sense if you are going to place the empty stuff back, you obviously can walk and return the containers when they are not empty.

Why are those of you who complain the loudest about supply X being low the same people who never place orders for anything?

Why do you not log off the lab computers? Do you know anyone can access your personal files? Do you realize when you are over your quota and someone else needs the computer they are going to dump your files to log you off so they can log on?

And why do you think your experiment is more important than any others in the lab? Do you realize many of us talk to one another and let each other know if we are using reagent Y, equipment Z, etc. and you know plan our experiments out beforehand and not just do things on the fly?

Please if you do not understand this, you are part of the problem. Please talk with a lab-mate and listen to what they have to say.

With much disgust,

Pondering Fool

Denialists...

2007-03-23T14:18:00.000-05:00

The Hoofnagles (Mark and Chris) have started a denialism blog Their take on the common denialists found online:
"HIV/AIDS Denialism - seems to feed into some egomania of this particular type of denialist. They frequently make statements about how one day they'll be vindicated, and seen as heroes because they saw the truth first. They also seem to really like inversions, and to feel superior because they believe in something that no one else does. Other conspiracy theorists, such as 9/11 conspiracy theorists, I think are similar. There is an egotistical appeal to possessing "secret" knowledge or holding controversial opinions. Basically, I'm calling them assholes.

Global Warming denialism - motivations seem to range from financial (industry, their lobbyists and think tanks), to individual cognitive dissonance. Many global warming denialists that argue from a non-financial standpoint seem to fear the changes that reducing a carbon footprint entails, and are concerned about losing quality of life. Others, I think, suffer from the same egomania as the HIV/AIDS denialists like Monckton. Still others, most recently Falwell, seem upset from a religious perspective as it suggests humans could somehow harm God's creation or worse, that global warming might be a positive sign of Armageddon.

Creationism/Intelligent Design Denialism - Almost exclusively religious objections, stemming from cognitive dissonance from fear of non-literal interpretation of the bible. The insistence on believing the truthfulness of some of the more absurd stories of the Bible such as Noah's Ark seems indicative of a certain stubbornness and fear of upsetting the fragile balance of the literalist's world view. The idea that the Bible might contain metaphor, rather than absolutes, is therefore terrifying and ideas such as evolution, that appear to negate the creation myth must be opposed at all costs.

Holocaust Denial - Hopefully we won't have to cover this disgusting kind of denialism as much. Its motivations are perhaps the clearest of them all. It's just plain Antisemitism.

Anti-Vaccination denialists - I have less experience with these but it seems mostly to be fearfulness of science, and a propensity towards believing in what Orac would call "woo". A small amount also seems to be paranoia or paranoid personality disorder. Finally, I think many of the parents of autistic children seem fearful of genetic or environmental causes of autism that might implicate their culpability in their child's illness. Sadly, throughout the history of autism parents have often been blamed, specifically absent fathers and cold or "Frigidaire" mothers were implicated. So it's understandable if people still feel some stigma or guilt from such a diagnosis given such a cruddy history from the psychologists on that one. Many parents would like to believe in something, anything that explains why their child has been singled out by nature to have autism. Having something to blame, like a vaccination, therefore becomes emotionally very appealing and alleviates some of the helplessness or misplaced guilt they may feel.

Animal testing denialists - I am somewhat uncertain about inclusion of some animal rights activists (ARAs) into the denialism camp. My reasons for doing so include the general dismissiveness I've seen of science by ARAs. For instance, saying things like science can be done without animals (or worse on a computer), claims from PETA that chickens are as smart as dogs or babies, that dogs are actually vegetarians (oy), and any number of discussions in which they imply that animals or animal models say nothing helpful about biology. Their motivations, for the most part, are more noble, they're interested in alleviating suffering, all suffering. That this is impossible, misguided or unwise is not important, and if they have to lie about science then so be it."

Choosing a lab...

2007-03-22T08:43:00.000-05:00

Since starting my post-doc, the lab I am in has had a couple of other post-doc candidates come visit. Soon it will be time for the 1st year grad students in the department to pick which lab they will work away in for the next four to six years. Whenever either happens inevitably the discussion of how to choose a lab comes up. It is not a choice to be made lightly. I have seen friends in grad school who choose the wrong lab and were tormented for years. Their PIs being masters at undermining confidence leading to the students feeling trapped. At the same time, I have seen people who realize the lab is not the right fit (usually the PI is a perfectly fine person, just not the best mentor for said student) and switch to another lab without a problem. Ideally you want to avoid the latter and most definitely the former is to be avoided if you can.

I know people who say you should join the most prestigious lab you can. The idea being you will have great connections and a good shot at papers in high impact journals. I personally think this is a bad way to choose a lab. To me the most important criteria is whether this is a lab you can see yourself working in for the next 4-6 years. Does it fit your learning style? Personality? If a PI is a micro-manager and you prefer some space, it probably is not going to be a good fit. If you need someone pushing you then a PI who is more hands-off is not the mentor for you. If you are open to possibilities outside of becoming a faculty member at a research university in the future, would the PI be supportive? If the answer is no, you should look for another lab. Does the PI care if you work 50 hours/week instead of 80 hours?

I am a big fan of talking with people who are in the lab, who have been in the lab, and those who choose not to join the lab. Find out why the made that choice and whether they would do it again. A warning sign if you are visiting as a post-doc is if the PI only lets you talk with certain people in the lab and not others. Typically this indicates they are hiding the malcontents. Ask yourself if the people in the lab are people who you wouldn't mind being around for the next few years. First years have a slight leg up on post-docs since grad students typically rotate in labs before picking one, giving them time to truly get a sense of the lab & the personalities in it. Lab feel is subjective. You have to know yourself which takes a certain level of maturity and confidence. You have to remind yourself it is your education, your training, your future especially when others are doubting your choice. Other factors should come in mind but they should be used to decide which of the good labs for you that you should join.

Factors in choosing a lab (in order of importance in my mind):
1) Fit - A) Will the PI be a good mentor for you? B) Is the lab environment conducive to you learning, working and keeping your sanity?

2) Science- does the work interest you? excite you? You are going to be working on these projects. If it doesn't excite you then you probably won't want to be there for long.

3) Funding- What is the grant situation looking like? A great lab fit-wise that is hoping to tackle exciting topics but without money it isn't going to happen. Not to mention it can be demoralizing.

4) Prestige- Connections do not hurt and high impact articles do help down the line but they are not everything.

Any I am missing? Let me know.

I typically (not all) find the PIs who sell prestige as being the most important are usually the one's to be watchful of before joining. They try to sucker students/post-docs in with talk of Science & Nature papers. Be skeptical if that is their biggest selling point. Remember if they want you to join their lab it means they think you could do high quality work, that they see your talent and that you are valuable. Guess what? If you join a different lab that is a better fit personality-wise, most likely you will do high quality work there as well but will be a happier person. Life is too short to waste it on taskmasters who want to use your abilities to keep their own prestige high.

Now picking a lab is not perfect. Remember plenty of successful scientists have changed labs and done well. If a lab is not working for you, you can switch. It will work. It won't set you back.

Programs need to remind Post-docs and grad students of this fact. Obviously the poor mentors are not going to.

Updated as per the suggestions of Katie at Minor Revisions:

There are a couple other things to keep in mind when joining a lab.
A) Lab space- Does the lab have physical space for you? Will you have your own desk? Bench space? What are the common areas like in the lab? Now part of this falls under funding but there are times when labs expand quicker than lab space is given. When I first joined my grad school lab, I had to share a desk and lab bench space. It sucked but I knew it was a two month situation until a visiting scientist and a couple post-docs moved on. For other labs this can be a common problem and people are placed in random spaces in the building, sometimes isolated from the rest of the lab. Some like this, other sdo not. Once again it is subjective based on what you can tolerate and what works best for you.

B) Politics- This ties into the lab environment and the science. Your work is not done in isolation. Your lab will be in a building with others and be part of a department/program/etc. You may collaborate with others. There are other people in the field. It can be tricky. Is there support for you beyond your lab? Support to teach you how to navigate turf wars? In a collaboration is everything clear on who is working on what? How authorship will be taken care of? Are there common resources you can utilize to make your life easier in the department (or will they make your life harder)?

C) Is the lab organized? Are there lab responsibilities that are evenly assigned? Do they have regularly scheduled research meetings/journal clubs? Are they productive meetings?

The key is asking lots of questions before joining a lab. Find out as much as you can to make an informed decision. Find out what is beneath the glitter to see if it would be actually gold for you.

On papers...

2007-03-20T05:46:00.000-05:00

It comes across listening to fellow grad students/post-docs at conferences, at graduate school, SnobU, etc. that different labs take very different approaches to getting work published. Some labs think in terms of the minimal publishable unit (MPU) and set up their experiments accordingly when starting a project. This can lead to rapid publications though at the expense of well supported conclusions but if you can spin it well you can get away with it. The main competitor of my current PI is like that. Very well written work comes out of his/her lab with an exciting spin that the data doesn't quite support. The other extreme is doing experiments and letting the data take you where it leads. This is the ideal of the scientific method that is taught from primary school onwards. You have a hypothesis, you design experiments to test it and based on your results you refine/alter your hypothesis and design more experiments. Once you have enough support you write up and publish. The conclusions are usually very well supported. The danger is getting scooped by the MPUers in the meantime on certain parts of your project, lessening the impact of your work. In addition you may have to go back and redo certain things to generate figures/tables that would fit the journal you are going to submit to though not adding any new results, just showing the ones you already have in a different way.

Most labs are not either but on spectrum between the two extremes. My lab is such a lab. We ask questions do initial experiments, generate results, ask more questions, etc. but at each point we sit down and talk with our PI about what will be publishable, thinking about where we would publish our work. As we generate more and more data we sit down and critically think about our projects, trying to think what a reviewer might say. Not just thinking of the experiments to be done but also how to present them and what journal we should submit to. Usually this speeds up our ability to publish while still having well supported conclusions. When the PI was having health problems & before I joined, the lab did publish a few MPU type papers. The conclusions of one were completely wrong. To my PI's credit, he/she went through the task of showing where we went wrong and doing the necessary work to reach a well supported conclusion.

Approaching writing a manuscript is also crucial. I know many labs try to shoot for the highest impact journal they can. The mindset being "it doesn't hurt to try". Actually, it does! Writing papers takes time. A Science paper is written and presented differently than a Biochemistry paper for example (not to mention the type of data tends to be different). If the paper is rejected, it means you have to rewrite the paper for a new journal. This resets the clock on the review process, further delaying your work being published. The rewriting also tends to take away time from designing/doing new experiments and/or having a life outside of lab. Not to mention, rejections can be demoralizing. On top of that, there is a good chance the reviewers will be the same. A couple rounds of submissions and these reviewers can tire of work, making it even harder to publish in the lower impact journals.

If you are in a competitive field, shooting too high can cost you. In the time that you are trying out journals, your competitors could publish similar work, scooping you while also having the time to start on the next round of experiments, setting you further back.

It is worth it therefore to sit down and really think about your work before writing. What are your main points you are making? What type of data do you have to support those points? What sort of impact does it make? What general scientific interest would it generate? Solicit the opinion of others. The work you are doing should be exciting and wonderful to you. That passion helps to motivate you to put the effort that is necessary but it does tend to make us less than objective about our own work. Listen to those you respect so you have a proper perspective. This is also very useful for those that tend to beat themselves up; don't undersell/shortchange your results and ideas either. Once you have a good idea what journal would accept your work, write a your manuscript accordingly. Have it read and edited by multiple people, multiple times. Make sure they are more critical than a reviewer (in a constructive way). Typically this approach leads to papers that are accepted with minimal revisions, saving you time to do more experiments and to have a life. The most successful PIs I have seen are the ones who learn this lesson early in their careers saving them time, money and maybe a little of their sanity.

Dr. Mom discusses impact scores further and where to submit your work in her wonderful Writing Your First Paper series.

A positive...

2007-03-18T10:07:00.000-05:00

A lot of what I write and link to is the negative in the world, thought I would point out a positive. Though the Christian Seniors organization might have a problem with Rep. Pete Stark being an atheist, they do not speak for everyone. The San Francisco Chronicle reports that most of the responses Rep. Stark has received have been positive and the few negative haven't been hate-filled rants but reasoned responses. In his own words, "In this instance, the people who have disagreed with me have been polite and reasonable. All in all, this has been a pleasurable experience.''

Rep. Stark being from the SF Bay Area probably is a major reason why he can state his non-beliefs without jeopardizing his career but good to know he isn't be sent hate messages from the rest of the world. A positive sign in this polarized religious world we live in.

Bigotry against non-believers...

2007-03-15T11:17:00.000-05:00

You can read on Pharyngula the reaction of some Christians to Rep. Pete Stark stating he did not believe in a deity. Got to love the bigotry.

This is why us atheists would like "under God" removed from the Pledge. Such phrases codify atheists and non-Judeo-Christians as unAmerican creating a breading ground for such bigotry. We are not asking for the line to be changed to "without God" but leaving the question to the individual. Of course when a leading candidate for the opposition party makes comments like this,"it is doubtful that children reciting the Pledge of Allegiance feel oppressed or brainwashed as a consequence of muttering the phrase "under God"" it is hard to overturn such a hateful tide.

Evidentily I made a carnival & request...

2007-03-15T05:33:00.000-05:00

I guess I made the Second Carnival of Scientiae. To the submitter of my post, thank you who ever you are. My blog tends to be my rants of the world around me and the elegance is not there yet, maybe someday. If you haven't checked out the links from Scientiae please do so, lots of great reads and things to ponder, not to mention to do something about.

The request-
Since I have a spike in traffic, I have a question of those who visit. How do you find new scientific papers to read? I have been using pubcrawler which searches pubmed (being a biochemist this does find most of the articles I am interested in) and sends the info of the latest papers from certain labs, on certain subjects, etc. everyday in the form of an e-mail. Does anyone know of a better service? Better method? Love to hear.

Round-up...

2007-03-14T18:02:00.000-05:00

Been busy writing a review and a couple of papers so here is a round-up of the brilliance of others.

P. Myers hosted an internet chat with Dr. Lynn Margulis. She raises important points as to our cultural biases potentially having an impact on how we view science (a very important reason why diversity is needed in the sciences, to get various viewpoints to help all of us overcome our individual biases). I do disagree with how far she takes it but it is something to keep in mind, especially those of us practicing science. On other things, it becomes clear just because you are brilliant doesn't mean you can't entertain wacky ideas (such as denying that there is strong evidence pointing to HIV causing AIDS). transcript and message from Dr. Marguilis.

Tara at Aetiology talks about Dr. Marguilis's comments. HIV denialists come right out of the woodwork, falling into the same mental traps as evolution-deniers.

Chad at Uncertain Principles is having way too much fun with brackets. one two three four five six seven eight March Madness anyone!?!? Reminds me I still need to do my bracket!

Female Science Professor discusses whether being honest about science discourages students from pursing graduate school/academic careers. IMHO, honesty is good but if you think someone can do it, also let them know that. All negative without positive reinforcement probably does discourage more than it should. Sugar-coating just sets people up for disappointment and bitterness which can be corrosive and depressing. The comments as always are great to read as the discussion moves into how poorly organized so many professors are, which does help to explain the long hours on the job by scientists.

The Science Professor brings up that there are different reasons why some labs become all male (demographic driven chance vs. negative environment for women) and the importance to deep digger into why that is before joining a lab.

Dr. Mom talks about who you teach to in a class and how. Issues like this are usually not discussed enough by science professors. Us scientists have much to learn about educating.

Science Woman is naming names and taking a stand against not giving pregnant women a fair chance to get a job. Unbelievable this person at the university did not accomadate. Wouldn't he want to cover his rear legally speaking at the very least?

Stupidity...

2007-03-09T13:23:00.000-05:00

PZ Myers has a fun little item. Can you count the ways they mess the science up in order to make a quick buck?

On tenure...

2007-03-09T06:37:00.000-05:00

Tenure recently it seems has caught fire on the the scienceblogs sparked in large part by Steve Levitt of Freakonomics fame blog on getting rid of it. I can't really speak to his arguments based on his experience as an Econ professor at University of Chicago, what I can speak to is tenure in the biological sciences. Jake Young at Pure Pedantry makes a case (in my opinion a poor and misinformed one) to junk it there as well.

Jake's first main point: "Tenure supports bad teachers as much as it supports unproductive researchers."

As others have noted, tenure does not correlate with the quality of teaching at an institution. Small liberal arts colleges which focus on undergraduate education have tenure but still maintain a high level of teaching quality even amongst those with tenure. Why? Because that is what is valued and selected for. Most research universities the focus is not undergraduate education it is research especially in the biomedical sciences. These institutions draw in significant amounts of money off of grants. At SnobU more revenue is made off of grants than each tuition/room & board combined, investment income and contributions. That is how a junior faculty member gets tenure by how much they bring in. Grants are not easy to get. The selection is therefore for faculty members who focus primarily on research, churning out high impact papers which in turn allows them to draw in grants. Faculty who are poor teachers get tenure. Sometimes it seems they are even more likely to get tenure because they are not "wasting their time" preparing great lectures and instead devoting the time to research. Even faculty who like to teach catch on pretty quick and perception becomes reality, they spend less time teaching and more time focussed on research. The selection at these research universities is therefore for faculty members who focus on research and view teaching as a "burden", an obligation to fulfill.

Tenure has nothing to do with it. Without tenure these institutions would still be selecting for professors that are successful at getting grants. There just wouldn't be any protection for faculty members to speak their minds, to challenge the administration when the administration is acting in its selfish short-term interests. Where I attended graduate school, the administration tried to cut the stockroom because it "cost" the university money (nevermind the overhead from the grants was paying for it). The stockroom because all items go to one location and buys in bulk is able to extract from companies great deals that can not be matched, saving labs significant amounts of money. The university only sees dollar signs though and doesn't care. They are getting their cut of the grants no matter what in their view so to them the stockroom is an expense they can cut. This would hurt the university, common items could not be picked up easily and prices would rise which would reduce the productivity of the labs. Down the road this would hurt chances the chances of faculty members to get grants and make the departments less attractive to grad students/post-docs/potential new faculty members. What saved the stockroom was senior faculty members rallying and making this exact point showing the administration that the bean-counters they were listening to don't know the whole story. The added twist is that the bean-counters are the same people who negotiate at a university wide level and they were not able to get the same deals as the stock-room, so the bean-counters had extra incentive to try and get rid of the stockroom which was making them look bad.

The junior faculty could not do this because they did not have tenure. Those that did were able to speak their minds thus preventing the university from being too corporate and shooting itself in the foot. Which brings up one of the other reasons Jake thinks tenure can & should go: "I don't buy the argument about academic freedom at all. "

Academic freedom is not just about being able to put forth controversial ideas without fear of being fired (which is an important part of the deal) but it is also about faculty members having a say in how the university runs; challenging the administration, allowing for a true free market of ideas when it comes to the direction of the institution. Many times it isn't the big fight but the little things that add up over time.

The last thing Jake brings up is the unproductive tenured researcher taking a slot away from a deserving junior faculty member ("Tenure -- like Social Security -- is something I never expect"). In the biological sciences, which Jake is in, this is an absurd argument. Faculty members have to stay productive in order to get grants which helps pay their salaries. Faculty members without grants do not get as much money and usually are pushed out by the university. I have watched it happen. They are pushed into worse & worse lab spaces that get smaller and smaller sometimes having to share space with multiple other professors in the same boat. This is done to make room for the new blood. It motivates the other senior faculty who fear that happening to them, encouraging them to work even harder out of fears of agism. Most universities do not have a slot system (I think Yale still does but is talking of getting rid of it). Your "slot" is not being taken up by some tenured unproductive faculty member. The lack of positions is based on the economics of it all. More labs means more costs without an offsetting increase in grant money as the labs are smaller which is not good for the bottom line of these research universities. Don't blame tenure for this. It is an easy target and diverts from the real problems in academia- universities run like corporations instead of places of higher learning.

In science you move around a lot between grad school, post-doc and starting a junior faculty position. Most people at a certain point want to settle down. Tenure offers that reward for working hard. It is the carrot. Salary alone for many would not make up for that. Get rid of tenure and you probably would decrease the pool of people who would be interested in the sciences. It would become a greater mountain to climb. Who would this affect the most? My bet, those that already have a higher mountain to climb to begin with (see below) de facto making science even more white and male. I don't think putting a greater selective pressure for white males is a way to improve science. Want to improve science? Level the playing field and let women & minorities equally compete with white males. That is not happening now and therein lies a major problem that goes with the corporatization of academia that is affecting the sciences in the US that Jake does raise. Tenure though is not the problem.

Political compass...

2007-03-08T19:47:00.000-05:00

Where I fall on the politcal compass:
Your political compass

Economic Left/Right: -9.00
Social Libertarian/Authoritarian: -8.41

I am more of a leftie than Mandela, Ghandi and the Dalai Lama and more libertarian then them as well. I basically have no one to vote for in the US.

Lab rants...

2007-03-08T07:47:00.000-05:00

Why in the world can't people put broken glass in the broken glass container and pippette tips in their proper waste container? Why must they insist on mixing the two? Not to mention regular trash? Are they trying to see how durable my hands are? Do they want me to bleed? At least they are not treating the chemical spill kit as a waste basket anymore. It is the little things...

A related rant, why in the world is the trash taken out only twice a week at SnobU? How much money goes from our grant to cover overheard? How much money does SnobU have in its endowment? Labs generate waste, we try not to. We try and recycle what we can but we still generate loads of trash. We can not have our trash bins overflowing in lab especially when a state inspector is coming. When I started at SnobU, the waste was taken during the week everyday. Usually done at hours when no one was in lab. Now, it is Tuesdays and Thursdays mid-morning while people are working. Our floors used to be cleaned at night/early in the morning. The last stop was our lab so when I got in really early I could see the facilities worker at work trying his best to get our floors nice and shiny. I watched him work very hard with a poor piece of equipment SnobU provided. He was always trying to come up with better ways to get the floors clean with the out-of-date equipment, it was impressive especially considering how little SnobU was paying him. Since his shift ended after his kids were already off to school, he would call them every morning and talk to them. Now SnobU has hired out. They have nicer equipment but they insist on cleaning floors around 5pm to 6pm. There are a number of people still working in lab at that time, it can be a hassle. If you do leave, you have to be very careful otherwise you might slip on the still very wet hallways as they start for some reason in the hallways and in front of the doors out. Got to love a university run like a corporation-less service at the same/higher price. Got to pay the execs what they are "worth" after all.

Some interesting reads (Catch-Up Edition)...

2007-03-06T06:35:00.000-05:00

Joolya has a Gender Studies Crash Course that all of us, in particular us men, need to read & reread on a constant basis. Patriarchy while giving men an advantage in society & oppressing women, limits all and leaves power in the hands of just a few. That society paradigm reiterates itself at all levels, preventing a true dialog between people so necessary for a truly democratic society. To make that a reality occur quicker, us men have to learn at most times when we normally speak, to shut-up and think before we say anything and at times we are normally quiet to actually say something (after thinking of course).

Larry Moran over at Sandwalk brought up the difference between the Central Dogma of Molecular Biology and the Sequence Hypothesis (what usually in textbooks passes as the Central Dogma of Molecular Biology). For those who teach from a textbook please read and go back to the source material & update your lectures. The Central Dogma is basically a negative statement that once sequence information flows from nucleic acid to protein it can not flow back nor from protein to protein. As for the Sequence Hypothesis- "In its simplest form it assumes that the specificity of a piece of nucleic acid is expressed solely by the sequence of its bases, and that this sequence is a (simple) code for the amino acid sequence of a particular protein." (Crick, F.H.C. (1958) On protein synthesis. Symp. Soc. Exp. Biol. XII:138-163).

Crick did update his version of The Central Dogma in a 1970 Nature article where he also reiterated the difference between the Central Dogma and the Sequence Hypothesis, an article to check out.

Moran also challenges the Three Domain Hypothesis though I think there is a bias there as even Doolittle as of 2006 that Eubacteria and Archaea were distinct, separate domains. Gene transfers does make it difficult to really get at the root of the tree of life to the last universal common ancestor or common ancestral state (LUCA/LUCAS). The main difficulty is where you place eukaryotes relative to archaea and bacteria & that is where most of the fuss really is. I will post about this latter.

Biocurious and The Daily Transcript point out the absurdity of how an academic publisher fighting open access journals like those from PLoS.

Dr. Mom has a great series on Writing Your First Paper as well as a nice piece on getting a faculty package together.

Tara at Aetiology writes on a nice smack-down of Jon Wells lack of understanding biology while trying to critique it. Tara also gives a wonderful Introduction to Microbiology and Infectious Diseases.

Over on Pharyngula, Dr. Myers has a piece on a medical doctor who refuses service to those in need because of his Christian faith (though the MD might want to brush up on his Bible, as Dr. Myers notes). And some people wonder why some atheists are so angry.

Why a leftie does not vote Democratic (Repost)...

2007-03-03T20:31:00.000-05:00

Thoughts from Kansas had a good point awhile ago regarding the benefits of having a push from the left in American politics. In the late 19th and the first half of the 20th century, there was a serious progressive voting presence in the United States which acted to pressure the two major parties leading them (the Democrats and Republicans) to soften their stand on unions, labor laws, voting rights and other progressive issues.

From 1904 through the 1924 presidential election, Socialist candidates were able to get at least 2.78% of the vote. The high was in 1912 with 6% of the vote going to Eugene Debs. The election was unique in that Teddy Roosevelt ran under the Progressive banner splitting the Republican vote allowing Woodrow Wilson to win. Many concessions were made to the progressives/socialists as the two major parties were trying to woe these progressive voters. The 16th Amendment established the right for Congress to enact income taxes, the 17th established the direct election of Senators and with the 19th women across the country gained the right to vote.

In 1924, the Progressive/Socialist coalition candidate, Robert LaFollette from WI, drew almost 17% of the vote and even got 13 electoral college votes. Many of their proposals in some form or another got folded into the New Deal. As FDR's New Deal expanded, the vote of the socialist candidates went down. In 1932 the Socialist candidate drew 2.2% of the vote by 1944 they were getting only 0.16% of the vote (WWII also playing a role).

In 1948 concerns about a Post-War economic slowdown and the Cold War gave rise to many 3rd parties. The Socialists drew only 0.28% of the vote. The Progressives drew about 2.38% of the vote though. This was countered though by the rise of the States' Rights (pro-segeragation) candidacy of Strom Thurmond who drew about 2.41% of the vote. In 1968, Wallace under the American Independent banner (once again pro-segeragation) received about 13.6% of the vote. The "States' Rights" movement drew from the Southern Democrats and was a reactionary response to the Civil Rights movement playing on the fears many white Protestants in the South had regarding Blacks and the left.

The Republicans, under Nixon, undertook the Southern Strategy to get those "Dixiecrats" to vote Republican, a tradition that stands to this day (hence the continued visits of Republicans to Bob Jones' University).

Until Nader (and that is debatable), there haven't been any strong 3rd party progressive candidates for president. A note, Nader in 2000 got 2.7% of the vote. Anderson and Perot were right of center candidates which encouraged the two parties to become even more similar to one another. Many liberals derided Nader and blamed him for Gore loosing to Bush in Florida. Never mind the reality that significant numbers of registered Democrats did not vote in the 2000 election in Florida and the logic makes a big assumption that all the Nader votes would have gone to Gore. Kerry in 2004 ran as a "centrist" and lost not just the electoral count but also the popular vote. Bush (as previous Republicans had been trying to do) expanded the Southern Strategy to Middle America, playing once again on the fears of white suburban/rural Christians.

Progressives in this country can not just go along with the Democratic Party (especially when they put a pro-war candidate up for president against the Republican pro-war president, when a good chunk of the nation was against the war). They must push for a strong third party candidate of their own. Force both parties to take notice. Change the nature of the debate. The politics of Bush is a direct result of the rightward push from the States' Rights movement of Thurmond's and Wallace's runs for the White House. Fears were played to and not confronted. What have many progressives done? Cower around the Democrats and agree to compromise. The problem is that is not something you compromise on, it is something you fight.

Has voting for Democrats in Congress stopped the War in Iraq? Has it ended the assults upon our civil liberties? Nope. Way to go.

What is fun is pointing this out to the fine folks over at the DailyKos.Tends to get the inmates a little rilied up.

(Presidential Election Info)

Women in science or Hey Larry don't you have a degree in Economics? (Repost)...

2007-03-03T20:08:00.000-05:00

Awhile ago, Dr. Myers over on Phayrngula has an interesting & disturbing piece on The cost of being a woman in science sparked by a correspondence to Nature entitled Mysterious disappearance of female investigators. It is about the worrying results of the first European Young Investigator awards. Women were severely underrepresented. The authors of the correspondence would like to study why this is the cause and replicate the work of C. Wennerås & A. Wold (Nepotism and sexism in peer review, view for free). The European Science Foundation (ESF) has refused to release any data to help the researches study the cause of the under representation of women in winning EYIAs.

Wold and Wennerås looked at peer-review evaluations to the Swedish Medical Research Council, including scores reviewers gave applicants for scientific competence, and compared those scores to more objective real world evaluations such as impact scores. What did they find? Something very disturbing:

"Did men and women with equal scientific productivity receive the same competence rating by the MRC reviewers? No! As shown in Fig. 1 for the productivity variable ‘total impact’, the peer reviewers gave female applicants lower scores than male applicants who displayed the same level of scientific productivity. In fact, the most productive group of female applicants, containing those with 100 total impact points or more, was the only group of women judged to be as competent as the least productive group of male applicants (the one whose members had fewer than 20 total impact points)."

They were also able to look at the impact of being a woman had on their competency evaluation for the grants:
"a female applicant had to be 2.5 times more productive than the average male applicant to receive the same competence score as he ((40+64)/40=2.6)."

In other words to get the same level of respect, women had to do basically 2.5 times more work to get this grant. Extrapolate out (which does appear to be the case I am afraid to say) to other grants/publications, etc. and you have a pretty good reason why so many women leave science. You have to get grants to stay in science. If the bar is raised higher for women then men, then men will get more grants and be more "successful". Not to mention who wants to put in 2.5 times more work to get the same reward? One has to be pretty passionate about science to do that. It is economics 101. We need to understand & appreciate the full extent of this problem, let the studies happen. It is the answer to the Larry Summers (an economist mind you) of the world.

Science and society as a whole is limited when we opress and exclude people for no reason other than they are not the dominate group. The enrichment for white guys means we are not getting the best and the brightest in the sciences not to mention lacking the full range of perspectives necessary for productive science.

Teaching Rant Part II (Repost)...

2007-03-03T20:01:00.000-05:00

So I am looking towards the future after graduate school. I would eventually like to get to get a faculty position at a small liberal arts college (SLAC). There are post-docs at such places where you get the chance to gain teaching experience & learn how undergrad directed research is done. What is the advice I am getting for doing a post-doc from those at SLACs? Do a traditional one and find teaching opportunities where I can in that framework (i.e. work tons of hours and throw teaching on top of that, I mean really who needs a life?). The research position will get me in the door more than teaching even though such a faculty position requires significantly more teaching than what is required of a faculty member at a research university. Doesn't seem to be the best system where no matter what career path you go with, doing a traditional post-doc is the door we all must go through. I like doing research but haven't really been given the chance to develop my teaching skills. Begs the questions, is grad school really teaching us what we need to know if everyone has to do more training afterwards? And is the training aspect of post-docs more BS than anything else? I am afraid to say yes. It is a system feeding off cheap labor who are passionate about science.

Teaching Rant Part I (Repost)...

2007-03-03T19:57:00.000-05:00

Awhile ago on Pharyngula it was brought up scientists do a poor job of outreaching to the public in general and in the course of discussing this that professors are not trained educators. Teaching is an art that requires a certain set of skills to go with a passion to teach and tremendous amounts of effort.

To become a life science professor, first you go to graduate school (well after years of schooling leading to an undergraduate degree). Your first year you take classes and rotate in various labs. After that you join a lab, pass qualifying exams, start your research and usually serve as a teaching assistant for a semester. Usually, you then TA one more semester and then do research until your research/thesis committee decides you have done enough to merit receiving a PhD. TAing is a requirement that is checked off. At SnobU, I took a "class" workshops to help me TA and become a better teacher. Who taught it? Other grad students who were teaching fellows for Grad Student center at SnobU. In other words, their training was not much beyond mine. They tried their best but in many respects it is the blind leading the blind. When TAing, based on my experience, professors do not provide much guidance. I gave a lecture, what advice did I get afterwards? Basically none.

After grad school, people post-doc where they do more research and try to make a name for themselves. Usually no teaching. One might supervise grad students/undergraduates but this typically ends up with the Post-Doc using them as an extra pair of hands because the pressure is to churn out data to in turn, turn out papers. Based on your research and potential to do research (i.e. get grants that bring dollars to the school), you get a position as a junior faculty member. Then you apply for grants, get a lab up and running, serve on committees, do research, write papers and as throw-in teach classes. Teaching is to be done but not at the expense of getting papers out and obtaining grants. Over time, you do less research and teaching and more of the administrative work. Tenure is primarily based on research not teaching. Throughout the process, people are selected mostly for their potential/ability to do research whereas teaching is viewed as a distraction from that goal.

Now some professors are able to do it all. Usually because they love teaching and value it. Those that really love teaching become professors at small liberal arts colleges where they can practice their art in an environment in which they are rewarded for teaching.

The upshot is though that most life science professors can not teach. They were never taught and have a hard time explaining their research to a larger audience. With the current attacks upon science, this is a major problem because scientists can not defend themselves because they lack the tools necessary. The poor teaching also means groups of students leave college without understanding what science is and basic scientific knowledge. Not to mention the numbers of students who run away from the sciences while in college.

On the other extreme, a significant percentage of middle and high school teachers are not properly trained in the sciences that they are teaching and/or are not given the resources they need to teach science and keep themselves current. (Another rant, why is it usually in high school, 2 years of science is required whereas 4 years of each English & Social Studies are required).

In the end how can we expect students to value learning from teachers when those at the highest levels of our education system do not value teaching?

Liberal Arts Colleges (Repost II)...

2007-03-03T19:08:00.000-05:00

Some links to various sites talking about how to become a faculty member in the sciences at a small liberal arts college.
Hunting for jobs in liberal arts colleges (Specifics for physics, but generally apply to all)
Uncertain Principles (A blog of a physics professor, Chad Orzel, at a LAC)
Pharyngula chimes in as well.

About the Annapolis Group, private LACS
Listing of the Annapolis Group
Public LACs

Pensions (Repost I)...

2007-03-03T19:01:00.000-05:00

The Wall Street Journal has a piece on liabilities associated with pensions which is usually used to explain why benefits for workers need to be reduced. The quick take home is that for many large corporations the liability comes not from the pensions for rank-n-file workers but rather from executive pensions. Many companies though report the two as one, making it seem has if the pension for the former is dragging down the company.

Some highlights (really lowlights):
"To help explain its deep slump, General Motors Corp. often cites "legacy costs," including pensions for its giant U.S. work force. In its latest annual report, GM wrote: "Our extensive pension and [post-employment] obligations to retirees are a competitive disadvantage for us." Early this year, GM announced it was ending pensions for 42,000 workers.

But there's a twist to the auto maker's pension situation: The pension plans for its rank-and-file U.S. workers are overstuffed with cash, containing about $9 billion more than is needed to meet their obligations for years to come.

Another of GM's pension programs, however, saddles the company with a liability of $1.4 billion. These pensions are for its executives."

In other words, GM is ending the pension for most of its workers, which it could afford while keeping the pension for its executives that is a liability on the company.

More:
"• Boosted by surging pay and rich formulas, executive pension obligations exceed $1 billion at some companies. Besides GM, they include General Electric Co. (a $3.5 billion liability); AT&T Inc. ($1.8 billion); Exxon Mobil Corp. and International Business Machines Corp. (about $1.3 billion each); and Bank of America Corp. and Pfizer Inc. (about $1.1 billion apiece).

• Benefits for executives now account for a significant share of pension obligations in the U.S., an average of 8% at the companies above. Sometimes a company's obligation for a single executive's pension approaches $100 million.

• These liabilities are largely hidden, because corporations don't distinguish them from overall pension obligations in their federal financial filings.

• As a result, the savings that companies make by curtailing pensions for regular retirees -- which have totaled billions of dollars in recent years -- can mask a rising cost of benefits for executives.

• Executive pensions, even when they won't be paid till years from now, drag down earnings today. And they do so in a way that's disproportionate to their size, because they aren't funded with dedicated assets."

"One reason executive pensions have grown so large is that they are linked to ballooning overall executive compensation. Companies often design retirement payouts to replace a percentage of what a person earns while active.

But for executives, the percentage of pay replaced is itself higher. Compensation committees often aim for a pension that replaces 60% to 100% of a top executive's compensation. It's 20% to 35% for lower-level employees."

And this:
"Pension plans, whether for executives or for others, are obligations to pay. In other words, they're debts. And like any debt, they have what amounts to a carrying cost. That carrying cost is part of a company's pension expense.

In the case of pensions for regular employees, the expense is partly or wholly offset by investment returns on money the company set aside in the pension plan when it "funded" it.

Executive pension plans are different. They're normally left unfunded. They have no assets set aside in them. That means there is no investment income to blunt the expense. The result is that obligations for executive pensions create far more expense for an employer, dollar-for-dollar, than pensions for regular workers.

A company's pension expense is something it has to subtract from its earnings each quarter. The cost of executive pensions, having no investment income to cushion it, hits the bottom line with full force."

Basically- executives per dollar of pension benefits costs the company more than a regular worker yet it is the pension of the latter group that is getting cut. Those that are the richest and who least need a pension get to keep their expensive pensions while workers are loosing their less expensive pension. Talk about living in loony world. Of course the reason this goes on, the executive pensions are for those who run the company. They are the ones deciding who gets what pay. Why would they cut back the money they make? In theory Board of Directors are supposed to keep this in check, though most of them are executives for their own companies. In other words they have incentive not to rock the boat. They are benefiting the same way.

"Companies generally are also free to alter, freeze or end regular employees' pension plans, unless a union contract is involved. But executive pensions often are protected from management interference by employment or other contracts."

In other words, workers to protect themselves need to unionize. It is the best protection your pension will have because the executives would love to raid it and give it to themselves.

Starting anew...

2007-03-01T19:24:00.000-05:00

I begin yet again. This is my second blog. The first has gone by the wayside. Some of the old posts will reappear shortly. Ranting is a tendency of mine and will probably occupy many of my posts. My grad schools days are now behind me and now I am a Post-Doc. Politically, I am a leftie, usually voting for candidates that most have never heard of. Some say I waste my votes but given the U.S. Constitution and gerrymandering, the way I view it, I would be anyway. I figure under such a scenario far better to stick to my principles and hopefully encourage 3rd party candidates to enter politics, changing the dynamics of the debate between Republicans and Democrats. It is a more long term view to politics than what is shown by the news networks.

I love science. Thinking and questioning the world around me was nurtered from a very early age by my parents. Research is fun but teaching science is my true joy. Nowhere as skilled as I would like as a teacher but always looking to improve which at my research university is far more challenging than it should.