In the comments to my earlier post on information management, Nat Blair wrote:
Here's another question though: what software do you use to store the tacit knowledge of the lab? Do you use a lab website to store some of that stuff? A lab wiki? Mostly just curious.
My answer at the time was that I wasn't using anything, but that I was considering implementing a wiki. There are a number of reasons why I hadn't implemented something. One was the draconian approach the administration here at Big State U. takes to any kind of web site created and maintained by faculty. A second was that implementing a wiki would require a substantial commitment of time on my part to get the software installed and running, plus an ongoing commitment to maintaining the software. I'm quite capable of doing this - I have a background in computational biology, although my lab is almost purely experiment-based now - but I'm not sure I can devote the time required. Nat's question did however spur me to spend some time looking for a simple solution. And I found one.
Google Sites.
There you can create a free web site with up to 100MB storage space. And, importantly, you can limit who can view and alter the site (e.g. upload or download stuff). Google (typically) provides a bunch of easy to use web-based tools for creating a site. So, with about two hours work I set up an intra-lab web site. I've uploaded many of our protocols and pdf's of some useful papers. There's a section including links to the web sites of the various vendors we commonly use. I've included a list gadget where any lab member can type in things that need to be ordered. Soon I hope to include a calendar gadget that will display everyone's schedules, including mine. It's a work in progress, but I think we're finally moving out of the dark ages with regard to lab information management.
Wednesday, November 05, 2008
Monday, November 03, 2008
How the hell did that get published?????? [Updated]
[DISCLAIMER: This post was prompted, in part, by recent posts over at Isis's temple and DrugMonkey's cage. One should not take the following as a comment on the paper under discussion there - I have not read it and it's way outside my area of expertise, so I'm not making any judgments about it whatsoever.]
All too often I find myself reading a peer-reviewed paper and wondering how on earth it managed to get by the reviewers and editor, and end up being published. In a reputable journal. I know many of my colleagues have the same experience.
I'm not necessarily talking about disagreeing with the interpretation of data. Rather, it's a matter of poorly executed, incorrect or missing experiments, lack of suitable controls, incorrect statistical analyses, egregious lack of, or incorrect, citation of other published work in the area, etc. In other words, truly bad papers.
How do these get published? I don't know, but I would like to offer a couple of suggestions based on my experiences on the editorial board of a mid-level journal. First up, let me state that I am a strong believer in the peer review process. I am also well aware that it has it's flaws. Secondly, a little background...
Here's how things are supposed to work at the Journal of Doodlewidgets. When a manuscript is submitted, the authors must supply the names of four potential reviewers plus suggest a member of the editorial board as someone suitable for handling the review process. The Editor then assigns the manuscript to an editorial board member (EBM), who may or may not be the one suggested by the authors. The EBM is then supposed to read the manuscript and decide if it's good enough to send out for review or whether it should be rejected without full review. Those manuscripts deemed good enough are then sent out for review. When the reviews are returned to the journal, the EBM makes a final decision (accept, reject, major or minor revisions) and the authors are informed. Many journals in my field have similar processes for handling submissions.
Here's where I see the system breaking down too often: at the EBM level on two counts.
1) As noted above, at the Journal of Doodlewidgets the EBM is supposed to read the manuscript and decide if it's good enough to send out for review. In other words, the EBM is supposed to perform a preliminary review of the manuscript. I suspect (know) this doesn't happen in many cases. There are those who join editorial boards just for the extra line on their CV's, and who can't be bothered with applying the required effort. It's not clear how to handle these people. The obvious answer is to boot them, but that's not so easy if the offending party is a Big Cheese. Journals like to have Big Cheese's on their boards for the cachet. And don't want the negative publicity that might occur if they boot a Big Cheese...
2) The bigger problem lies in the choice of reviewers. It's all too easy to send the manuscript out to two (or more) of the suggested reviewers. Problem is, those people are likely good friends of the authors. We all play that game. We suggest people we know who we think will review our manuscripts fairly. Or, in the case of a (hopefully) minority of authors, automatically favorably. In some cases, authors suggest ex-co-authors or collaborators. The corresponding author of a manuscript I handled recently listed as a suggested reviewer someone they were co-authors with on a manuscript in press! Needless to say that's just not on.
So, it's possible that a given manuscript receives reviews that are more positive than they should be, and the EBM (who hasn't bothered reading the manuscript) simply accepts them at face value. Or the EBM is good friend of one of the authors and over-rides a more negative review. Or, perhaps the manuscript is somewhat outside the EBM's area of expertise, in which case they assume the reviews from the suggested reviewers are legit. In the end, a substandard manuscript can end up being accepted...
Note that this is the opposite of the usual reviewing issue (reviewers being too harsh) often discussed on the blogosphere. And I'm ignoring the issues of lazy reviewers - a good EBM should pick up on those - or unqualified reviewers - which is the EBM's fault for using them.
It's not clear how to deal with this. If all EBM's were conscientious it wouldn't be much of an issue. But how do you ensure that the editorial board is stocked with only the good? I suspect Editors have some idea of who's dead wood, but since there are no good metrics for measuring EBM performance...
EBM's could ignore the list of suggested reviewers, but then what's the point of making authors go through that process? And most authors are probably making legitimate suggestions. You could simply scrap the idea of having a list of suggestions, but then it becomes a real crapshoot if you have a lazy or somewhat unqualified EBM handling your manuscript.
I don't know the best way to fix this, or even if it's as big an issue as I perceive it to be, but I do have three suggestions. The first is for EBM's to use at most only one of the suggested reviewers. Yes, that means making some EBM's work harder, but it's not that much effort. I know because this is what I do. My second suggestion is to require authors to submit a list of people who should be excluded from reviewing due to various conflicts of interest. By this I mean the kind of thing the NSF requires from people applying for a grant. A list of all co-authors and collaborators over the last four years. Plus postdoc and PhD mentors. Okay, so that's a bunch of work for the authors, but you do want that manuscript reviewed fairly, right? And you do want to see fewer crap manuscripts accepted, right? If you keep a running list, it's not that much work. Alternatively, suggesting inappropriate reviewers could be made grounds for immediate rejection, but that can be a difficult call for even the most conscientious EBM.
And finally, the EBM's name should be included in the paper. That alone should improve matters.
And thus endeth yet another long post.
All too often I find myself reading a peer-reviewed paper and wondering how on earth it managed to get by the reviewers and editor, and end up being published. In a reputable journal. I know many of my colleagues have the same experience.
I'm not necessarily talking about disagreeing with the interpretation of data. Rather, it's a matter of poorly executed, incorrect or missing experiments, lack of suitable controls, incorrect statistical analyses, egregious lack of, or incorrect, citation of other published work in the area, etc. In other words, truly bad papers.
How do these get published? I don't know, but I would like to offer a couple of suggestions based on my experiences on the editorial board of a mid-level journal. First up, let me state that I am a strong believer in the peer review process. I am also well aware that it has it's flaws. Secondly, a little background...
Here's how things are supposed to work at the Journal of Doodlewidgets. When a manuscript is submitted, the authors must supply the names of four potential reviewers plus suggest a member of the editorial board as someone suitable for handling the review process. The Editor then assigns the manuscript to an editorial board member (EBM), who may or may not be the one suggested by the authors. The EBM is then supposed to read the manuscript and decide if it's good enough to send out for review or whether it should be rejected without full review. Those manuscripts deemed good enough are then sent out for review. When the reviews are returned to the journal, the EBM makes a final decision (accept, reject, major or minor revisions) and the authors are informed. Many journals in my field have similar processes for handling submissions.
Here's where I see the system breaking down too often: at the EBM level on two counts.
1) As noted above, at the Journal of Doodlewidgets the EBM is supposed to read the manuscript and decide if it's good enough to send out for review. In other words, the EBM is supposed to perform a preliminary review of the manuscript. I suspect (know) this doesn't happen in many cases. There are those who join editorial boards just for the extra line on their CV's, and who can't be bothered with applying the required effort. It's not clear how to handle these people. The obvious answer is to boot them, but that's not so easy if the offending party is a Big Cheese. Journals like to have Big Cheese's on their boards for the cachet. And don't want the negative publicity that might occur if they boot a Big Cheese...
2) The bigger problem lies in the choice of reviewers. It's all too easy to send the manuscript out to two (or more) of the suggested reviewers. Problem is, those people are likely good friends of the authors. We all play that game. We suggest people we know who we think will review our manuscripts fairly. Or, in the case of a (hopefully) minority of authors, automatically favorably. In some cases, authors suggest ex-co-authors or collaborators. The corresponding author of a manuscript I handled recently listed as a suggested reviewer someone they were co-authors with on a manuscript in press! Needless to say that's just not on.
So, it's possible that a given manuscript receives reviews that are more positive than they should be, and the EBM (who hasn't bothered reading the manuscript) simply accepts them at face value. Or the EBM is good friend of one of the authors and over-rides a more negative review. Or, perhaps the manuscript is somewhat outside the EBM's area of expertise, in which case they assume the reviews from the suggested reviewers are legit. In the end, a substandard manuscript can end up being accepted...
Note that this is the opposite of the usual reviewing issue (reviewers being too harsh) often discussed on the blogosphere. And I'm ignoring the issues of lazy reviewers - a good EBM should pick up on those - or unqualified reviewers - which is the EBM's fault for using them.
It's not clear how to deal with this. If all EBM's were conscientious it wouldn't be much of an issue. But how do you ensure that the editorial board is stocked with only the good? I suspect Editors have some idea of who's dead wood, but since there are no good metrics for measuring EBM performance...
EBM's could ignore the list of suggested reviewers, but then what's the point of making authors go through that process? And most authors are probably making legitimate suggestions. You could simply scrap the idea of having a list of suggestions, but then it becomes a real crapshoot if you have a lazy or somewhat unqualified EBM handling your manuscript.
I don't know the best way to fix this, or even if it's as big an issue as I perceive it to be, but I do have three suggestions. The first is for EBM's to use at most only one of the suggested reviewers. Yes, that means making some EBM's work harder, but it's not that much effort. I know because this is what I do. My second suggestion is to require authors to submit a list of people who should be excluded from reviewing due to various conflicts of interest. By this I mean the kind of thing the NSF requires from people applying for a grant. A list of all co-authors and collaborators over the last four years. Plus postdoc and PhD mentors. Okay, so that's a bunch of work for the authors, but you do want that manuscript reviewed fairly, right? And you do want to see fewer crap manuscripts accepted, right? If you keep a running list, it's not that much work. Alternatively, suggesting inappropriate reviewers could be made grounds for immediate rejection, but that can be a difficult call for even the most conscientious EBM.
And finally, the EBM's name should be included in the paper. That alone should improve matters.
And thus endeth yet another long post.
Wednesday, October 29, 2008
Information management tools
The key to success as an academic scientist lies in successful management of two vital resources: time and information. Poor management of one or both of these will make success (as measured by the usual metrics of tenure, grants and publications) extremely difficult, if not impossible. I've been thinking about information management recently (I'll save time management for another post).
We live in the information age - ready access to the internet can easily lead to information overload, a debilitating condition that can lead directly to a lack of focus and an inability to act efficiently. This isn't the first time people have had to deal with information overload (or at least worried about it). James Burke notes in The Knowledge Web that the powers that be were concerned that the printing press would overload the citizens of the time with worthless knowledge (or more likely, knowledge the overlords would have preferred kept to themselves), so both church and state imposed strict censorship. Efforts to censor the internet have, so far, failed. In fact the internet has become such a ubiquitous part of our lives that I suspect any large-scale censorship efforts are doomed to fail.
So how to manage the vast amounts of information flooding our professional lives? Here I'm referring to external sources (i.e. not the flood of data from your lab). Buggered if I know a really good answer to that. I do know that the first step is to filter. Ruthlessly. The vast majority of the information flooding my academic life is useless, irrelevant and/or unimportant. Delete it. Block it. Just get rid of it. Otherwise you'll spend your days whacking useless moles.
Below I describe the tools and/or approaches I use to handle the bulk of the rest of the information. Your mileage may vary. I'd welcome comments from others describing other ways to handle this stuff. Note that I'm a Mac user, so some of the stuff I describe is Mac-centric.
Email
I find if I don't handle important emails within a day they tend to get ignored for too long. So I reply to the important stuff within a few hours when I can. Everything else is filed away or deleted. In some cases I've set up signatures I can use as a sort of form-letter reply, but I only use those for form-letter-style emails (e.g. the dozens of form-letter emails I get a week from people looking for a position in my lab).
And I make liberal use of Apple Mail's junk mail-learning feature.
I do tend to keep copies of most non-junk emails. I have set up numerous folders in Mail for this purpose. This has proven very useful at times when I've wanted to track down some piece of information I was sent some time ago.
iGoogle
I have a personalized home page I've set up with iGoogle. Right there on the front page I have gadgets for Google Reader, Google Calendar, Gmail Contacts, and gadgets I've created myself (a very easy process) for access to Big State U.'s web interface to email, links to my lab's homepage and various other links I use several times a day. My homepage also has a set of tabs linking to other personalized pages with gadgets for Google Docs and Google Notebook, various search engines (PubMed, Google Scholar etc.), the news, weather etc. etc. This is all very easy to set up and puts a whole bunch of stuff I use a lot all in one easy to access place. Furthermore, I can access it from any computer connected to the internet.
Google Reader
I love Google Reader. I have journal table of content feeds, grantmaking agency feeds, feeds from ISI's Web of Knowledge tracking citations to my published work, etc.* All in one place. Makes dealing with all that stuff really easy.
I just wish I could get my saved PubMed searches fed into Google Reader... Anyone know how to do that?
Calendars
Alright, so these are really time management tools, but they contain information too. I like iCal on the Mac. I have it synced with Google Calendar (via Busymac shareware - I'm too cheap to invest in MobileMe). This allows me to keep iCal on Macs at home and work all synced. And give me access to my calendars via my iGoogle home page. Any changes made to any of the calendars is automatically transmitted over the internet to the others. Cool.
Address Books
It's good to have the same address book on my Macs at work and home, my cell phone, and in Gmail Contacts. Good, but not as easy as I would like. My cell phone has Bluetooth, so that's not too bad. I did need a plugin to get it to play nice with Apple's iSync, but that was easy enough. Syncing the Mac Address book with Gmail Contacts isn't so easy (unless you have an iPhone or iPod Touch...). I use a little freeware program called A to G to help with this. Unfortunately any changes I make on either Mac or on Gmail Contacts isn't automatically transmitted to the others... Apparently this is being added to Busymac at some point. SpanningSync is another option for Mac users, but is a subscription service.
One day I'm getting me one of those newfangled iPhone gadgets...
Google Notebook
I've just started using this as a sort of glorified To Do device. I have notebooks with short-term plans for my various research projects, one for a new project I'm planning, one for non-research lab-related plans etc. The jury is still out on this one, but I like the idea of having ready access to this kind of stuff from where ever.
Bookmarks
You could keep track of bookmarks via Google, but I find that a little cumbersome. I use Firefox as my main browser and have downloaded an Add-In called Foxmarks. This syncs my bookmarks from Firefox on my Mac at work with that at home via the internet.
References
Back in the Dark Ages when I was a grad student I used to make photocopies of papers relevant to my research. This continued into my postdoc years. With the advent of PDF's I began printing them out. A lot of trees died. A lot. Early on as a postdoc I realized my ever-growing pile of papers was getting out of hand. So I hit on a system of labeling them before filing them away after reading. I started numbering them, starting at one. I'm now up to 2310 (I keep a note of where I am, and no, I haven't actually read all 2310 in detail, just most of them). That way I could file the papers numerically. At about the same time I started using EndNote. EndNote has a field called "Label" for each entry - that's where I put my numbers. So I can look up a paper in EndNote and find it in seconds in my files. In recent years I've tried to wean myself of the environmentally-unfriendly habit of printing out every paper I think I want to read. Instead I try to save and read the PDF on my computer. I rename each PDF with a number and enter it into EndNote with the number in the "Label" field. That way I can look it up and find it on my computer in seconds. And the Mac search feature, Spotlight, can be used to search via keywords etc. to dig up all papers related to a certain subject.
That's it for now. As I said above, I'd welcome comments from others describing other ways to handle this stuff.
Damn I'm getting into the habit of very long posts. Perhaps I should market them as a cure for insomnia...
* I like to know where my work has been cited. In part because it helps me keep track of the field, and in part because of vanity. :-)
We live in the information age - ready access to the internet can easily lead to information overload, a debilitating condition that can lead directly to a lack of focus and an inability to act efficiently. This isn't the first time people have had to deal with information overload (or at least worried about it). James Burke notes in The Knowledge Web that the powers that be were concerned that the printing press would overload the citizens of the time with worthless knowledge (or more likely, knowledge the overlords would have preferred kept to themselves), so both church and state imposed strict censorship. Efforts to censor the internet have, so far, failed. In fact the internet has become such a ubiquitous part of our lives that I suspect any large-scale censorship efforts are doomed to fail.
So how to manage the vast amounts of information flooding our professional lives? Here I'm referring to external sources (i.e. not the flood of data from your lab). Buggered if I know a really good answer to that. I do know that the first step is to filter. Ruthlessly. The vast majority of the information flooding my academic life is useless, irrelevant and/or unimportant. Delete it. Block it. Just get rid of it. Otherwise you'll spend your days whacking useless moles.
Below I describe the tools and/or approaches I use to handle the bulk of the rest of the information. Your mileage may vary. I'd welcome comments from others describing other ways to handle this stuff. Note that I'm a Mac user, so some of the stuff I describe is Mac-centric.
I find if I don't handle important emails within a day they tend to get ignored for too long. So I reply to the important stuff within a few hours when I can. Everything else is filed away or deleted. In some cases I've set up signatures I can use as a sort of form-letter reply, but I only use those for form-letter-style emails (e.g. the dozens of form-letter emails I get a week from people looking for a position in my lab).
And I make liberal use of Apple Mail's junk mail-learning feature.
I do tend to keep copies of most non-junk emails. I have set up numerous folders in Mail for this purpose. This has proven very useful at times when I've wanted to track down some piece of information I was sent some time ago.
iGoogle
I have a personalized home page I've set up with iGoogle. Right there on the front page I have gadgets for Google Reader, Google Calendar, Gmail Contacts, and gadgets I've created myself (a very easy process) for access to Big State U.'s web interface to email, links to my lab's homepage and various other links I use several times a day. My homepage also has a set of tabs linking to other personalized pages with gadgets for Google Docs and Google Notebook, various search engines (PubMed, Google Scholar etc.), the news, weather etc. etc. This is all very easy to set up and puts a whole bunch of stuff I use a lot all in one easy to access place. Furthermore, I can access it from any computer connected to the internet.
Google Reader
I love Google Reader. I have journal table of content feeds, grantmaking agency feeds, feeds from ISI's Web of Knowledge tracking citations to my published work, etc.* All in one place. Makes dealing with all that stuff really easy.
I just wish I could get my saved PubMed searches fed into Google Reader... Anyone know how to do that?
Calendars
Alright, so these are really time management tools, but they contain information too. I like iCal on the Mac. I have it synced with Google Calendar (via Busymac shareware - I'm too cheap to invest in MobileMe). This allows me to keep iCal on Macs at home and work all synced. And give me access to my calendars via my iGoogle home page. Any changes made to any of the calendars is automatically transmitted over the internet to the others. Cool.
Address Books
It's good to have the same address book on my Macs at work and home, my cell phone, and in Gmail Contacts. Good, but not as easy as I would like. My cell phone has Bluetooth, so that's not too bad. I did need a plugin to get it to play nice with Apple's iSync, but that was easy enough. Syncing the Mac Address book with Gmail Contacts isn't so easy (unless you have an iPhone or iPod Touch...). I use a little freeware program called A to G to help with this. Unfortunately any changes I make on either Mac or on Gmail Contacts isn't automatically transmitted to the others... Apparently this is being added to Busymac at some point. SpanningSync is another option for Mac users, but is a subscription service.
One day I'm getting me one of those newfangled iPhone gadgets...
Google Notebook
I've just started using this as a sort of glorified To Do device. I have notebooks with short-term plans for my various research projects, one for a new project I'm planning, one for non-research lab-related plans etc. The jury is still out on this one, but I like the idea of having ready access to this kind of stuff from where ever.
Bookmarks
You could keep track of bookmarks via Google, but I find that a little cumbersome. I use Firefox as my main browser and have downloaded an Add-In called Foxmarks. This syncs my bookmarks from Firefox on my Mac at work with that at home via the internet.
References
Back in the Dark Ages when I was a grad student I used to make photocopies of papers relevant to my research. This continued into my postdoc years. With the advent of PDF's I began printing them out. A lot of trees died. A lot. Early on as a postdoc I realized my ever-growing pile of papers was getting out of hand. So I hit on a system of labeling them before filing them away after reading. I started numbering them, starting at one. I'm now up to 2310 (I keep a note of where I am, and no, I haven't actually read all 2310 in detail, just most of them). That way I could file the papers numerically. At about the same time I started using EndNote. EndNote has a field called "Label" for each entry - that's where I put my numbers. So I can look up a paper in EndNote and find it in seconds in my files. In recent years I've tried to wean myself of the environmentally-unfriendly habit of printing out every paper I think I want to read. Instead I try to save and read the PDF on my computer. I rename each PDF with a number and enter it into EndNote with the number in the "Label" field. That way I can look it up and find it on my computer in seconds. And the Mac search feature, Spotlight, can be used to search via keywords etc. to dig up all papers related to a certain subject.
That's it for now. As I said above, I'd welcome comments from others describing other ways to handle this stuff.
Damn I'm getting into the habit of very long posts. Perhaps I should market them as a cure for insomnia...
* I like to know where my work has been cited. In part because it helps me keep track of the field, and in part because of vanity. :-)
Saturday, October 25, 2008
Dear Graduate Student...
At Big State U. all graduate students have an advisory committee that generally consists of their mentor, two (sometimes three) other faculty from their department and one person from outside their department. Right now I'm the outside person on three such committees. Two years ago I was part of the qualifying exam for one of these students. I came very, very close to failing her at the time because she demonstrated an almost complete lack of knowledge regarding some of the methods she was using. I happen to know quite a bit about those techniques since I helped develop them. I believed at the time that that's why I was asked to be on this committee. Apparently not. The student was surprised to find out I knew something about these techniques... Anyway, I passed the student in the end because she seemed to have a pretty good grasp of the other aspects of her proposed research. I told the student I would be more than willing to help her understand and use the techniques in question. I have seen nothing of her since (she's in a different building on a different part of campus so there's very little chance of running into her).
Now here at Big State U. graduate students typically have a meeting once a year with their committee to keep the members updated on the student's progress. Students are also encouraged to talk to their committee members on a regular basis (although distressingly few do so). Last December I remembered that we should have probably had a meeting with this student by then, and emailed her asking her if she would be setting one up soon. She replied that she hadn't really thought about it, but that it might be a good idea... Nothing further happened.
In April she sent out an email to her committee asking when they would be available to meet. Now asking four faculty members when they're available without providing potential times never works. I and one of the other committee members both replied that it would be a good idea for the student to provide a list of potential times so committee members could then indicate which would work. She replied that this seemed like a good idea... Nothing further happened.
About ten days go (it's October now) I get this email from said graduate student:
Dear Dr. Odyssey,
I am beginning my job search and would like to use you as a reference.
Sincerely,
Graduate Student
Here is the ensuing email conversation that occurred:
Dear Graduate Student,
I am very surprised to hear that you are looking for a job. I assume that means you believe you will be graduating soon. I'm afraid that I cannot agree to act as a reference for you since I have no idea of how your research has been progressing. We have not had a committee meeting in two years and I have not seen you in that time.
I am also puzzled that you seem to believe you will be graduating soon. Typically the student needs the okay of their committee before starting to write their dissertation. I strongly suggest that you set up a meeting as soon as possible so that you can discuss this with your committee.
Sincerely,
Dr. Odyssey
Dear Dr. Odyssey,
I have not been able to set up a committee meeting over the last two years because I haven't been able to find a time when both I and Dr. Mentor's Other Graduate Student can have a meeting at the same time. Other Graduate Student has three committee members in common with me and we want to save them time by having a committee meeting together.
I will be starting to write my dissertation by the beginning of November and hope to set up my dissertation defense for February.
I will do my best to set up a meeting by the end of the year or early next year. You can decide then whether you will act as a reference for me.
Sincerely,
Graduate Student
Note: I am not on Other Graduate Student's committee. I strongly suspect the one person on that committee who is NOT on Graduate Student's committee is the outside person. It pretty much has to be.
Dear Graduate Student,
You really cannot have a committee meeting with Other Graduate Student. Each student needs to meet with their committee separately. I happened to run into one of your other committee members today and he has assured me that he does not want a joint meeting with Other Graduate Student.
Additionally, perhaps you did not quite understand my last email. Here at Big State U. you need your dissertation advisory committee to agree before you start writing your dissertation. Although this is generally a given, it cannot occur without a meeting of the committee. You need to set up a committee meeting as soon as possible.
Finally, I stand by my decision not to act as your reference. I have had no contact with you in two years and do not feel I could write a reasonable letter.
Dr. Odyssey
Dear Committee Members,
I am hoping to set up a meeting sometime in the next six weeks. When are you available?
Sincerely,
Graduate Student
Sigh... I sent her an extensive list of times I would be available.
About five days pass with no further emails from Graduate Student. Then, late yesterday:
Dear Dr. Odyssey,
I cannot set up a committee meeting at this time. The one member of Other Graduate Student's committee who is not on my committee is traveling and hasn't replied to our emails.
Sincerely,
Graduate Student
I haven't replied as yet... Obviously a call to Dr. Mentor is overdue. I strongly suspect that some of this is driven by Dr. Mentor, so it won't be a comfortable call.
Oh, and I do understand that I and the other committees members share some blame here. We have not been particularly aggressive in trying to get Graduate Student to organize meetings and I haven't made any efforts to meet one-on-one with her.
Now here at Big State U. graduate students typically have a meeting once a year with their committee to keep the members updated on the student's progress. Students are also encouraged to talk to their committee members on a regular basis (although distressingly few do so). Last December I remembered that we should have probably had a meeting with this student by then, and emailed her asking her if she would be setting one up soon. She replied that she hadn't really thought about it, but that it might be a good idea... Nothing further happened.
In April she sent out an email to her committee asking when they would be available to meet. Now asking four faculty members when they're available without providing potential times never works. I and one of the other committee members both replied that it would be a good idea for the student to provide a list of potential times so committee members could then indicate which would work. She replied that this seemed like a good idea... Nothing further happened.
About ten days go (it's October now) I get this email from said graduate student:
Dear Dr. Odyssey,
I am beginning my job search and would like to use you as a reference.
Sincerely,
Graduate Student
Here is the ensuing email conversation that occurred:
Dear Graduate Student,
I am very surprised to hear that you are looking for a job. I assume that means you believe you will be graduating soon. I'm afraid that I cannot agree to act as a reference for you since I have no idea of how your research has been progressing. We have not had a committee meeting in two years and I have not seen you in that time.
I am also puzzled that you seem to believe you will be graduating soon. Typically the student needs the okay of their committee before starting to write their dissertation. I strongly suggest that you set up a meeting as soon as possible so that you can discuss this with your committee.
Sincerely,
Dr. Odyssey
Dear Dr. Odyssey,
I have not been able to set up a committee meeting over the last two years because I haven't been able to find a time when both I and Dr. Mentor's Other Graduate Student can have a meeting at the same time. Other Graduate Student has three committee members in common with me and we want to save them time by having a committee meeting together.
I will be starting to write my dissertation by the beginning of November and hope to set up my dissertation defense for February.
I will do my best to set up a meeting by the end of the year or early next year. You can decide then whether you will act as a reference for me.
Sincerely,
Graduate Student
Note: I am not on Other Graduate Student's committee. I strongly suspect the one person on that committee who is NOT on Graduate Student's committee is the outside person. It pretty much has to be.
Dear Graduate Student,
You really cannot have a committee meeting with Other Graduate Student. Each student needs to meet with their committee separately. I happened to run into one of your other committee members today and he has assured me that he does not want a joint meeting with Other Graduate Student.
Additionally, perhaps you did not quite understand my last email. Here at Big State U. you need your dissertation advisory committee to agree before you start writing your dissertation. Although this is generally a given, it cannot occur without a meeting of the committee. You need to set up a committee meeting as soon as possible.
Finally, I stand by my decision not to act as your reference. I have had no contact with you in two years and do not feel I could write a reasonable letter.
Dr. Odyssey
Dear Committee Members,
I am hoping to set up a meeting sometime in the next six weeks. When are you available?
Sincerely,
Graduate Student
Sigh... I sent her an extensive list of times I would be available.
About five days pass with no further emails from Graduate Student. Then, late yesterday:
Dear Dr. Odyssey,
I cannot set up a committee meeting at this time. The one member of Other Graduate Student's committee who is not on my committee is traveling and hasn't replied to our emails.
Sincerely,
Graduate Student
I haven't replied as yet... Obviously a call to Dr. Mentor is overdue. I strongly suspect that some of this is driven by Dr. Mentor, so it won't be a comfortable call.
Oh, and I do understand that I and the other committees members share some blame here. We have not been particularly aggressive in trying to get Graduate Student to organize meetings and I haven't made any efforts to meet one-on-one with her.
Friday, October 10, 2008
Notes from a small meeting
I'm back. Did you miss me?
Overall the meeting in the Armpit of the Midwest went very well (for me). I came away with a seminar invitation, ideas for a couple of cool experiments to do, and a bunch of good suggestions/ideas relating to my fledgling new research program. I also had a very informative and productive two hour lunch with Mega-Big Cheese (recent NAS inductee), Super Big Cheese and Former Postdoc Mentor (also a Super Big Cheese). To what extent I swayed the NSF review panel members who were there is an unknown of course. I've done what I can and now it's time to focus on getting stuff done for the resubmission should it be necessary...
Here are some observations from the meeting:
* And before anyone leaps to the conclusion that this is sour grapes on my part, I organized this meeting a few years ago and am therefore not eligible to organize it again. That's how this one works.
Overall the meeting in the Armpit of the Midwest went very well (for me). I came away with a seminar invitation, ideas for a couple of cool experiments to do, and a bunch of good suggestions/ideas relating to my fledgling new research program. I also had a very informative and productive two hour lunch with Mega-Big Cheese (recent NAS inductee), Super Big Cheese and Former Postdoc Mentor (also a Super Big Cheese). To what extent I swayed the NSF review panel members who were there is an unknown of course. I've done what I can and now it's time to focus on getting stuff done for the resubmission should it be necessary...
Here are some observations from the meeting:
- When giving a 30 minute talk, it's probably not a good idea to spend 20 minutes introducing a subject that everyone in the audience has a good grasp of, 2 minutes on data and 8 on (over-reaching) conclusions... It would have been one thing if a graduate student had done this, but sadly it was a rather senior and well-known PI.
- If you're attending a highly-focused meeting on thingamabobs and present a poster on doozits (which aren't related to thingamabobs at all), don't be surprised if very few people show any interest. And don't spend the remainder of the meeting complaining loudly that very few people showed interest.
- If you're organizing a small meeting and want to have all of the talks loaded onto a single laptop, make the laptop available to speakers more than five minutes before each session starts. And use a PC (or at the very least warn all speakers in advance that you're going to use a Mac). I'm a Mac person, but even I recognize that, thanks to Micro$oft, Powerpoint slides made on a PC often don't work on a Mac, whereas the opposite usually (not always) works. It was very painful watching two inexperienced graduate student speakers struggling with screwed up slides that were prepared on a PC but didn't work on a Mac. And it wasn't their fault - they weren't given the time to look over their slides on the Mac prior to their talks.
- If you're organizing a small meeting, don't insist all talks are loaded onto one laptop. Get a switch.
- Just because you used to be a Big Cheese (no, you used to be one, but really aren't anymore - study sections have been telling you that for a decade, and rightly so) does not mean you get to ask off-topic questions after every talk.
- It's okay to canvass the powers that be to elect you organizer for next year's meeting. That's how it works. It's not okay, after being elected, to tell everyone that you didn't canvass. It's a small group. We're all aware of who does what. Now you look like a jackass.*
- Poster making is an art form. There's a lot of really bad art out there. Really bad.
- The right amount of beer + the right amount of wine = good science. Usually. Too much beer + too much wine + one graduate student = a messy job for the janitor.
* And before anyone leaps to the conclusion that this is sour grapes on my part, I organized this meeting a few years ago and am therefore not eligible to organize it again. That's how this one works.
Friday, October 03, 2008
The Armpit of the Midwest
Tomorrow I leave for a small, but extremely good, meeting being held just outside a small city I refer to as the Armpit of the Midwest. There are worse body parts you could name a city after, so clearly this isn't the worst place in the Midwest. But it's not great. Obviously I'm not going for the location. No, this is a very good small meeting that is not advertised, so it's kind of clubby, but is extremely rigorous. The most rigorous meeting I know of. The participants all tend to be good-natured, but present a poor or incorrect analysis, or inappropriate statistical analysis (or heaven forbid no statistical analysis!) and they will hand you your head on a platter. After having sliced, diced and julienned it. Followed by a quick puree. In the nicest possible way of course.
This is where I'm hoping to bolster the chances of my recently submitted NSF proposal. At least two of the review panel members will be there. I didn't get as much done as I had hoped - the central protein in my new research direction is a pain in the butt to make. I have managed to improve our expression and purification protocols to the point where we're getting a yield 3-4 times larger than at the time of grant submission. This was important because biophysical work can require a lot of material. And we've finished a couple of new experiments, but not the ones I had hoped to do. Oh well, I have what I have.
This is an important reason for attending meetings. Meetings are useful for improving the odds of getting funded. One could even view this as the main reason to attend a meeting. You should aim to impress the people who will/are reviewing your proposals. Your goals are to convince them that you're someone worth funding and, if you have a proposal pending, that you are making progress.
Hopefully I can do the above in the Armpit of the Midwest.
This is where I'm hoping to bolster the chances of my recently submitted NSF proposal. At least two of the review panel members will be there. I didn't get as much done as I had hoped - the central protein in my new research direction is a pain in the butt to make. I have managed to improve our expression and purification protocols to the point where we're getting a yield 3-4 times larger than at the time of grant submission. This was important because biophysical work can require a lot of material. And we've finished a couple of new experiments, but not the ones I had hoped to do. Oh well, I have what I have.
This is an important reason for attending meetings. Meetings are useful for improving the odds of getting funded. One could even view this as the main reason to attend a meeting. You should aim to impress the people who will/are reviewing your proposals. Your goals are to convince them that you're someone worth funding and, if you have a proposal pending, that you are making progress.
Hopefully I can do the above in the Armpit of the Midwest.
Sunday, September 21, 2008
Two parties
Nope, not the political kind. A couple of weeks ago I was at a graduate student's oral qualifying exam. After we had all asked questions and it was clear that the the student had passed with flying colors, one of the other faculty asked the following question (accompanied with the qualifier that the student's answer's had no bearing on whether or not they passed):
You are going to hold two dinner parties. For the first you can invite any four scientists, living or dead. For the second, any four famous people who are/were not scientists, living or dead. Who would you invite and why?
I forget the student's precise answers, and for this post they're not important anyway. The first party was a test of the student's breadth of knowledge of science in general (including it's history). The second had to do with the student's knowledge of topics other than science. The faculty member wanted to stress the importance of knowing much more than just your own narrow little area of research.
I think I would invite the following (putting aside all potential communication issues):
Science soiree:
Josiah Willard Gibbs - he was the most under-appreciated theorist of his time. Perhaps ever.
James Clerk Maxwell - not just a famous theoretical physicist, but also a poet! Albeit not a great one... And a contemporary of Gibbs.
John Edsall - a protein chemist's physical chemist. I had the pleasure of meeting him once. A wonderful gentleman.
J. Robert Oppenheimer - someone who went from being the most influential scientist of his time to a victim of McCarthyism has got to be worth a dinner party. And he hiked around Corsica with John Edsall when they were both young.
Hmmm, obviously I have a thing for the physical sciences...
Celebrity carouse:
Ludwig von Beethoven - how he wrote his Ninth Symphony while deaf is something that has always fascinated me.
Picasso - no doubt he would keep the conversation interesting (and wine flowing).
Euripides - of the few authors of Greek tragedies whose work has survived, he is my favorite.
Charles Dickens - despite the best efforts of my high school English teachers, I really enjoy his books and their insight into Victorian England.
So, dear readers, who would you invite and why?
You are going to hold two dinner parties. For the first you can invite any four scientists, living or dead. For the second, any four famous people who are/were not scientists, living or dead. Who would you invite and why?
I forget the student's precise answers, and for this post they're not important anyway. The first party was a test of the student's breadth of knowledge of science in general (including it's history). The second had to do with the student's knowledge of topics other than science. The faculty member wanted to stress the importance of knowing much more than just your own narrow little area of research.
I think I would invite the following (putting aside all potential communication issues):
Science soiree:
Josiah Willard Gibbs - he was the most under-appreciated theorist of his time. Perhaps ever.
James Clerk Maxwell - not just a famous theoretical physicist, but also a poet! Albeit not a great one... And a contemporary of Gibbs.
John Edsall - a protein chemist's physical chemist. I had the pleasure of meeting him once. A wonderful gentleman.
J. Robert Oppenheimer - someone who went from being the most influential scientist of his time to a victim of McCarthyism has got to be worth a dinner party. And he hiked around Corsica with John Edsall when they were both young.
Hmmm, obviously I have a thing for the physical sciences...
Celebrity carouse:
Ludwig von Beethoven - how he wrote his Ninth Symphony while deaf is something that has always fascinated me.
Picasso - no doubt he would keep the conversation interesting (and wine flowing).
Euripides - of the few authors of Greek tragedies whose work has survived, he is my favorite.
Charles Dickens - despite the best efforts of my high school English teachers, I really enjoy his books and their insight into Victorian England.
So, dear readers, who would you invite and why?
Monday, September 15, 2008
Five year plans
I had mentioned the use of a five year plan in a previous post describing my mid-tenure crisis. An anonymous commenter asked:
I was just curious about your 5 year plan...how detailed is it? For example, do you plan out the number of pubs per year? Do you plan out which/how many grant deadlines to target? (All Without knowing how the data will turn out!)
...which spurred this post.
I first came across the idea of a five year plan in Kathy Barker's At the Helm. I would recommend anyone about to start their own lab get a copy of this. I don't have my copy in front of me right now and I don't remember precisely what she says about five year plans (other than she recommends having one), so the following are my thoughts likely heavily tinged with hers.
Some opening points.
1) Not everyone will find this useful. Some/many people are quite good at managing their academic careers without something like this. I wish I were one of them.
2) This is something that needs to be referred to often and requires constant updating. Like your CV. You do update your CV regularly, don't you?
3) This is a medium- to long-term planning tool (i.e. six months up to five years). Anything short-term (less than six months) probably belongs in a calendar.
Why have a five year plan?
The simple answer is to get to where you want to be.
If you can't picture precisely where you want to be and what you want to be doing in five years, you need to figure out a) where and what, and b) how you're going to get there (i.e. a plan). Writing it down helps. If you can picture the where and what, you probably still need a plan.
Note that I used the word want above. No one can guarantee where you'll be and what you'll be doing. What is guaranteed is that you won't arrive at your destination without constantly thinking about how you'll get there.
What should be in it?
Anything that helps. But it must be obtainable. And somewhat specific ("get tenure", although obviously a great goal, isn't specific enough to be of any use). Entries must have definable target dates (which can be somewhat fuzzy, e.g. "late 2010"). What ends up in a five year plan is going to depend on where you are in your career and what the demands of your particular field are.
I use three (not mutually exclusive) categories for entries: Research, Career, and University.
Research
This includes anything research-related. Most of my entries involve funding. Be reasonable here. Yes, it would be nice to have:
Fall 2009: Get R01 for work on thingamajigs.
But being realistic, I would have:
Fall 2009: Submit R01 proposal for work on thingamajigs.
I also outline possible specific aims under a grant entry. These tend to change as the work evolves.
I also follow up with entries like:
Spring 2010: Resubmit R01 proposal for work on thingamajigs if necessary.
Something else I've included in my plan is a major equipment proposal for a time-resolved fluorimeter. This is something we don't have that would be very useful in my work. It would also be useful for others on my campus. So I have a set of goals with deadlines leading up to submitting such a proposal. One such goal was to organize a group of funded PI's who would benefit from this instrument. I've done that and that item has been deleted from my plan.
I do not include publishing research papers. I seriously doubt anyone can predict what research papers they will publish two, three, or more years from now. On the other hand, I would include plans for reviews and/or book chapters.
Career
Here I include anything to do with forwarding my career (other than the Research items above). Here I included getting myself on a Society committee (I was a little too enthusiastic with this and ended up on two...), some specific networking goals (I suck at networking...), volunteering for a foundation review panel, etc.
University
This category contains anything related to teaching and/or service within Big State U. For example, I recently became course director for an advanced graduate level course that had been stagnating for some years. I have goals for what I want the course to become and have entries in my five year plan dealing with each goal.
I also run a NSF-REU site and have specific goals for that outlined.
I do keep track of the goals I've met and those I haven't. As long as the former greatly outnumber the latter I figure I'm doing okay.
And that's it really. Nothing earth-shattering. Just a list of reasonable goals that help keep me on track.
Hmmm, the above sounds rather like an entry in a self-help book. Sorry about that.
I was just curious about your 5 year plan...how detailed is it? For example, do you plan out the number of pubs per year? Do you plan out which/how many grant deadlines to target? (All Without knowing how the data will turn out!)
...which spurred this post.
I first came across the idea of a five year plan in Kathy Barker's At the Helm. I would recommend anyone about to start their own lab get a copy of this. I don't have my copy in front of me right now and I don't remember precisely what she says about five year plans (other than she recommends having one), so the following are my thoughts likely heavily tinged with hers.
Some opening points.
1) Not everyone will find this useful. Some/many people are quite good at managing their academic careers without something like this. I wish I were one of them.
2) This is something that needs to be referred to often and requires constant updating. Like your CV. You do update your CV regularly, don't you?
3) This is a medium- to long-term planning tool (i.e. six months up to five years). Anything short-term (less than six months) probably belongs in a calendar.
Why have a five year plan?
The simple answer is to get to where you want to be.
If you can't picture precisely where you want to be and what you want to be doing in five years, you need to figure out a) where and what, and b) how you're going to get there (i.e. a plan). Writing it down helps. If you can picture the where and what, you probably still need a plan.
Note that I used the word want above. No one can guarantee where you'll be and what you'll be doing. What is guaranteed is that you won't arrive at your destination without constantly thinking about how you'll get there.
What should be in it?
Anything that helps. But it must be obtainable. And somewhat specific ("get tenure", although obviously a great goal, isn't specific enough to be of any use). Entries must have definable target dates (which can be somewhat fuzzy, e.g. "late 2010"). What ends up in a five year plan is going to depend on where you are in your career and what the demands of your particular field are.
I use three (not mutually exclusive) categories for entries: Research, Career, and University.
Research
This includes anything research-related. Most of my entries involve funding. Be reasonable here. Yes, it would be nice to have:
Fall 2009: Get R01 for work on thingamajigs.
But being realistic, I would have:
Fall 2009: Submit R01 proposal for work on thingamajigs.
I also outline possible specific aims under a grant entry. These tend to change as the work evolves.
I also follow up with entries like:
Spring 2010: Resubmit R01 proposal for work on thingamajigs if necessary.
Something else I've included in my plan is a major equipment proposal for a time-resolved fluorimeter. This is something we don't have that would be very useful in my work. It would also be useful for others on my campus. So I have a set of goals with deadlines leading up to submitting such a proposal. One such goal was to organize a group of funded PI's who would benefit from this instrument. I've done that and that item has been deleted from my plan.
I do not include publishing research papers. I seriously doubt anyone can predict what research papers they will publish two, three, or more years from now. On the other hand, I would include plans for reviews and/or book chapters.
Career
Here I include anything to do with forwarding my career (other than the Research items above). Here I included getting myself on a Society committee (I was a little too enthusiastic with this and ended up on two...), some specific networking goals (I suck at networking...), volunteering for a foundation review panel, etc.
University
This category contains anything related to teaching and/or service within Big State U. For example, I recently became course director for an advanced graduate level course that had been stagnating for some years. I have goals for what I want the course to become and have entries in my five year plan dealing with each goal.
I also run a NSF-REU site and have specific goals for that outlined.
I do keep track of the goals I've met and those I haven't. As long as the former greatly outnumber the latter I figure I'm doing okay.
And that's it really. Nothing earth-shattering. Just a list of reasonable goals that help keep me on track.
Hmmm, the above sounds rather like an entry in a self-help book. Sorry about that.
Friday, September 05, 2008
Tuesday, September 02, 2008
Sounds like science
Why is this thus? What is the reason for this thusness?
Artemus Ward, US humorist (1834 - 1867)
Thursday, August 21, 2008
Mid-tenure crisis
I have a confession to make. About a year ago I had managed to put myself in a position that should be avoided at all costs. In regards to my research program, I had become...
complacent.
This is a bad, bad thing that no PI should ever do. I had been cruising along for about 7-8 years working away on a system, publishing a decent number of decent papers that garnered decent citations. Then about a year ago I was sitting on a bus going from Forsaken Conference Site in New England to the Boston airport. Sitting next to me was my good friend Rising Star Theoretician. RST turned to me and said, in more or less these words, "Your research program is going nowhere and you're in danger of becoming irrelevant." This was neither easy to hear, nor easy for RST to say. But he was right. Deep down I had known this for at least two years, but things were trundling along okay, so there was no immediate incentive to do anything about it. RST reminded me that there is always incentive to tend to the future of your research program. Having a future research program is the incentive.* I will always be in debt to RST for giving me a verbal kick in the pants.
I got lucky twice here. The first time was with RST's pep talk. The second time was a few months after that. I had just read a paper written by Benevolent Bioscientist, someone who had co-founded the field I was hoping to develop my new research program in. For reasons that are still unclear to me, BB had befriended me about a year previously and so I now knew him quite well. Anyway, the predictions he had made in this paper struck a chord. THIS was where I was headed. Or at least, some part of it. So I called BB to chat about his paper and the many opportunities it offered. BB told me I should work on protein X (one of the opportunities outlined in his paper). He said "I've been meaning to work on X for 10-15 years now and, to be honest, I don't think I'm ever going to get around to it. You should do it. Let me know how I can help." I knew protein X was important and I knew this was a generous offer. What I didn't quite grasp at the time was how important protein X is, and consequently how generous a gift this was. Protein X is a key player in not just one, not just two, but numerous disease states, including mental, cardiac and immune system disorders. And it's not understood at the molecular level. Protein X is an untapped goldmine that will lead to publications that are much more than "decent." And will lead me to NIH funding (I'm NSF-funded because of the nature of my previous work).
So here we are about a year after RST's pep talk. The old research program is (in hindsight predictably) rapidly dying. I have about one more decent publication I can squeeze out of that work. The all new research program based on protein X is still in its infancy, but it's growing stronger each day. Working on protein X has meant learning a whole new set of skills (I didn't train as a protein chemist), but fortunately I'm surrounded by colleagues who are willing to help. The timing is unfortunate (purely my own fault). I had to submit a renewal of my NSF grant in mid July. Obviously it had to be on protein X (there's plenty of basic science regarding X). It's not clear I had quite enough preliminary data (protein X is difficult to make because of its interesting properties), so I may be facing a funding gap for the first time.** But I'm having a blast in the lab. In fact, I'm more enthusiastic about my research than I have been in years. Staring from scratch again has been, and continues to be, hard. But I'm having fun.
* Have a written five year plan. It sounds dorky, but it works, and it should cover all aspects of your academic career. Read it and update it often. Never let your plan fall below the five year mark. If you can't see where your research might be five years from now, start developing a new research project with long term potential. Now.
** I'm working hard to avoid this. I will put in the two page update in the Fall, although I'm well aware those don't buy you much. More importantly I'll be presenting our data on protein X at a small meeting in early October. A number of the review panel members will be there, as will at least two of the people I suggested as reviewers (NSF does use reviewer suggestions - you'd be a fool not to provide some). With the exception of a much-needed two week vacation, since July I've been busting my guts making protein X and doing experiments. Come the end of September I will have the data. I hope.
This is a bad, bad thing that no PI should ever do. I had been cruising along for about 7-8 years working away on a system, publishing a decent number of decent papers that garnered decent citations. Then about a year ago I was sitting on a bus going from Forsaken Conference Site in New England to the Boston airport. Sitting next to me was my good friend Rising Star Theoretician. RST turned to me and said, in more or less these words, "Your research program is going nowhere and you're in danger of becoming irrelevant." This was neither easy to hear, nor easy for RST to say. But he was right. Deep down I had known this for at least two years, but things were trundling along okay, so there was no immediate incentive to do anything about it. RST reminded me that there is always incentive to tend to the future of your research program. Having a future research program is the incentive.* I will always be in debt to RST for giving me a verbal kick in the pants.
I got lucky twice here. The first time was with RST's pep talk. The second time was a few months after that. I had just read a paper written by Benevolent Bioscientist, someone who had co-founded the field I was hoping to develop my new research program in. For reasons that are still unclear to me, BB had befriended me about a year previously and so I now knew him quite well. Anyway, the predictions he had made in this paper struck a chord. THIS was where I was headed. Or at least, some part of it. So I called BB to chat about his paper and the many opportunities it offered. BB told me I should work on protein X (one of the opportunities outlined in his paper). He said "I've been meaning to work on X for 10-15 years now and, to be honest, I don't think I'm ever going to get around to it. You should do it. Let me know how I can help." I knew protein X was important and I knew this was a generous offer. What I didn't quite grasp at the time was how important protein X is, and consequently how generous a gift this was. Protein X is a key player in not just one, not just two, but numerous disease states, including mental, cardiac and immune system disorders. And it's not understood at the molecular level. Protein X is an untapped goldmine that will lead to publications that are much more than "decent." And will lead me to NIH funding (I'm NSF-funded because of the nature of my previous work).
So here we are about a year after RST's pep talk. The old research program is (in hindsight predictably) rapidly dying. I have about one more decent publication I can squeeze out of that work. The all new research program based on protein X is still in its infancy, but it's growing stronger each day. Working on protein X has meant learning a whole new set of skills (I didn't train as a protein chemist), but fortunately I'm surrounded by colleagues who are willing to help. The timing is unfortunate (purely my own fault). I had to submit a renewal of my NSF grant in mid July. Obviously it had to be on protein X (there's plenty of basic science regarding X). It's not clear I had quite enough preliminary data (protein X is difficult to make because of its interesting properties), so I may be facing a funding gap for the first time.** But I'm having a blast in the lab. In fact, I'm more enthusiastic about my research than I have been in years. Staring from scratch again has been, and continues to be, hard. But I'm having fun.
* Have a written five year plan. It sounds dorky, but it works, and it should cover all aspects of your academic career. Read it and update it often. Never let your plan fall below the five year mark. If you can't see where your research might be five years from now, start developing a new research project with long term potential. Now.
** I'm working hard to avoid this. I will put in the two page update in the Fall, although I'm well aware those don't buy you much. More importantly I'll be presenting our data on protein X at a small meeting in early October. A number of the review panel members will be there, as will at least two of the people I suggested as reviewers (NSF does use reviewer suggestions - you'd be a fool not to provide some). With the exception of a much-needed two week vacation, since July I've been busting my guts making protein X and doing experiments. Come the end of September I will have the data. I hope.
Monday, August 18, 2008
I'm a such a geek...
Scientists for Better PCR
My favorite lines:
"PCR when you need to find out who your Daddy is... (Who's your Daddy.)"
My favorite lines:
"PCR when you need to find out who your Daddy is... (Who's your Daddy.)"
Tuesday, August 12, 2008
Bad Science
I'm back from vacation. It's amazing what lying on a beach watching the waves can do for your mental health. Not to mention the restorative effects of good food and libations. I have colleagues who firmly believe that if you wish to be successful you cannot afford to take vacations. I counter with if you wish to stay sane and productive, how can you afford not to take vacations?
While enjoying the beach I managed to finish reading Gary Taubes' Bad Science: The Short Life and Weird Times of Cold Fusion which was published way back in 1993. Remember the whole cold fusion debacle? In 1989 Stan Pons and Martin Fleischmann of the University of Utah announced via a press conference that they had observed nuclear fusion at room temperature in what amounted to little more than a sophisticated test tube. Taubes, a science journalist who publishes in places like Science, wrote this book about the whole affair including the work of many groups who tried to replicate the cold fusion experiment. It's a fascinating read. I was absolutely astounded by the shear volume of bad science that resulted from the Pons and Fleischmann announcement. A surprisingly large number of scientists who should have known better claimed to have observed cold fusion in some form or another without having performed any controls. And furthermore, no one was able to reproduce the effect consistently. In many cases they couldn't reproduce their results at all... Cold fusion clearly was complete nonsense and perhaps even constituted fraud on the part of some of its proponents. I would recommend people read this book, especially science students. It is a wonderful description of how science should not be done.
At one point in his book Taubes ponders why scientists tend to react so violently to bad/fraudulent science. The answer is quite simple really. We all need to trust the results of other scientists. Science is built upon science. We have neither the time nor resources to replicate all the experiments that our own work is built upon. Sure, experiments that appear to point to amazing breakthroughs or are counter to current dogma will be replicated (or at least people will attempt to do so). But the vast majority of the data published by scientists is assumed to be good data. So we get really, really pissed off when it's not.
Perhaps surprisingly, perhaps not, the cold fusion field is still alive...
While enjoying the beach I managed to finish reading Gary Taubes' Bad Science: The Short Life and Weird Times of Cold Fusion which was published way back in 1993. Remember the whole cold fusion debacle? In 1989 Stan Pons and Martin Fleischmann of the University of Utah announced via a press conference that they had observed nuclear fusion at room temperature in what amounted to little more than a sophisticated test tube. Taubes, a science journalist who publishes in places like Science, wrote this book about the whole affair including the work of many groups who tried to replicate the cold fusion experiment. It's a fascinating read. I was absolutely astounded by the shear volume of bad science that resulted from the Pons and Fleischmann announcement. A surprisingly large number of scientists who should have known better claimed to have observed cold fusion in some form or another without having performed any controls. And furthermore, no one was able to reproduce the effect consistently. In many cases they couldn't reproduce their results at all... Cold fusion clearly was complete nonsense and perhaps even constituted fraud on the part of some of its proponents. I would recommend people read this book, especially science students. It is a wonderful description of how science should not be done.
At one point in his book Taubes ponders why scientists tend to react so violently to bad/fraudulent science. The answer is quite simple really. We all need to trust the results of other scientists. Science is built upon science. We have neither the time nor resources to replicate all the experiments that our own work is built upon. Sure, experiments that appear to point to amazing breakthroughs or are counter to current dogma will be replicated (or at least people will attempt to do so). But the vast majority of the data published by scientists is assumed to be good data. So we get really, really pissed off when it's not.
Perhaps surprisingly, perhaps not, the cold fusion field is still alive...
Monday, July 28, 2008
Thursday, July 24, 2008
In praise of small grants
Yesterday I was informed that I was awarded a small grant. It's only $35k/yr. for two years. Still, that's enough to pay for a pair of hands in the lab for two years. It's enough to get a new project up and running, and to generate the preliminary data needed for a large grant application. And it's enough to keep my lab afloat should my NSF renewal (submitted last week) not be funded first time through.
Many department chairs (and deans) in colleges of medicine tend to think it's NIH R01's or nothing. Maybe an NSF grant, but clearly that's 2nd class money. Small grants such as those given out by many foundations? Complete waste of time. This is a very short-sighted view and, when NIH funding rates are low as is currently the case, can be damaging. Fortunately my chair doesn't think that way. And of course neither do I. In fact my chair, despite having 3 R01's, still applies for the occasional small grant. He uses them to try out new projects/ideas.
Don't get me wrong. One can't, and shouldn't attempt to, run a research program funded solely by small grants. And you cannot, and shouldn't, be awarded tenure if that's all the funding you have (at least not in a research intensive science department). And deans tend to dislike them because they either don't pay indirect costs or pay a small percentage.
[For my non-science readers, indirect costs are funds taken from a grant to pay for infrastructure (ie electricity, phone service, buildings, maintenance etc.). Dean's like this money - the more they have, the more power they have. Hence their dislike of grants that don't provide such funds.]
Still, small grants are wonderful things. As I noted above, they're good for starting new projects, paying for an extra warm body, and, if necessary, bridging lapses in more major funding.
Many department chairs (and deans) in colleges of medicine tend to think it's NIH R01's or nothing. Maybe an NSF grant, but clearly that's 2nd class money. Small grants such as those given out by many foundations? Complete waste of time. This is a very short-sighted view and, when NIH funding rates are low as is currently the case, can be damaging. Fortunately my chair doesn't think that way. And of course neither do I. In fact my chair, despite having 3 R01's, still applies for the occasional small grant. He uses them to try out new projects/ideas.
Don't get me wrong. One can't, and shouldn't attempt to, run a research program funded solely by small grants. And you cannot, and shouldn't, be awarded tenure if that's all the funding you have (at least not in a research intensive science department). And deans tend to dislike them because they either don't pay indirect costs or pay a small percentage.
[For my non-science readers, indirect costs are funds taken from a grant to pay for infrastructure (ie electricity, phone service, buildings, maintenance etc.). Dean's like this money - the more they have, the more power they have. Hence their dislike of grants that don't provide such funds.]
Still, small grants are wonderful things. As I noted above, they're good for starting new projects, paying for an extra warm body, and, if necessary, bridging lapses in more major funding.
Monday, July 14, 2008
Cover your butt syndrome
I have a grant from the National Science Foundation, a Federal agency, to run a Research Experiences for Undergraduates (REU) site. Basically this lets me bring eight undergraduate students into the Department to do research for ten weeks during the Summer. The grant pays them a stipend and covers the cost of staying in the dorms for ten weeks. On Friday afternoon I had an interesting phone call from the University accounting office:
After introductions and various pleasantries...
Accounting drone: "We have a bill from University housing that they want to charge to your NSF REU grant. We need you to send us a written justification for paying for dorm housing on a grant. And we need it in the next hour or so - this is the last day we can pay this off the last financial year of the grant."
Me: "There's a specific budget line item for covering these costs. We justified that when we applied for the money. And it's a requirement of the NSF that we provide dorm housing."
Accounting drone: "We still need a justification for why you're paying for dorm housing on a grant."
Me: "This is a grant for training undergraduate students and requires us to provide dorm housing. I don't understand why you need a justification when we already had to provide that when we applied for the grant."
Accounting drone: "It's in case we're audited."
Me: "Audited by whom?"
Accounting drone: "The Federal government."
Me: "Let me get this straight, you need me to justify spending Federal grant money on dorm housing mandated by the Federal agency that provided the grant in case the Federal government decides to audit us because the University is afraid that such a Federal audit might get it into trouble if we didn't justify spending Federal dollars on Federally-mandated dorm housing?"
Accounting drone: "Yes."
Me: "I see..."
To her credit, this was not accounting drone's fault, and she did send me a copy of someone else's justification to copy from (there's more than one REU site on campus). But still...
After introductions and various pleasantries...
Accounting drone: "We have a bill from University housing that they want to charge to your NSF REU grant. We need you to send us a written justification for paying for dorm housing on a grant. And we need it in the next hour or so - this is the last day we can pay this off the last financial year of the grant."
Me: "There's a specific budget line item for covering these costs. We justified that when we applied for the money. And it's a requirement of the NSF that we provide dorm housing."
Accounting drone: "We still need a justification for why you're paying for dorm housing on a grant."
Me: "This is a grant for training undergraduate students and requires us to provide dorm housing. I don't understand why you need a justification when we already had to provide that when we applied for the grant."
Accounting drone: "It's in case we're audited."
Me: "Audited by whom?"
Accounting drone: "The Federal government."
Me: "Let me get this straight, you need me to justify spending Federal grant money on dorm housing mandated by the Federal agency that provided the grant in case the Federal government decides to audit us because the University is afraid that such a Federal audit might get it into trouble if we didn't justify spending Federal dollars on Federally-mandated dorm housing?"
Accounting drone: "Yes."
Me: "I see..."
To her credit, this was not accounting drone's fault, and she did send me a copy of someone else's justification to copy from (there's more than one REU site on campus). But still...
Wednesday, July 09, 2008
Wednesday, July 02, 2008
I never win anything
I have a much less than stellar record when it comes to winning things. Contests, lotteries, gambling of various sorts. It's not clear to me whether fate is conspiring against me or I'm just a living demonstration of the odds against winning those sorts of things...
But things can change. I just won a blue one of these! The 8GB version. Just for filling out a survey for a foundation that supports research into a particular disease. Happy, happy, joy, joy!
But things can change. I just won a blue one of these! The 8GB version. Just for filling out a survey for a foundation that supports research into a particular disease. Happy, happy, joy, joy!
Subscribe to:
Posts (Atom)