Tuesday, June 26, 2007

Review already in...

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

Saturday, June 23, 2007

Why an advisor with connections is good...

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

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

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

Monday, June 18, 2007

Group meetings...

How do other people's labs handle group meetings?

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

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

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

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

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

One paper down...

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

Friday, June 8, 2007

Chemical lab safety...

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

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

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

Proposed list find anything that is in your lab?

Tuesday, June 5, 2007

Ranking graduate programs...

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

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

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

And I am sure there are tons more possibilities.

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

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

Saturday, June 2, 2007

Movie round-up...

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

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

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

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

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

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