Open Thread

January 23, 2015

Whatcha got today, folks?

57 Responses to “Open Thread”

  1. Dr Becca Says:

    SkyMall went bankrupt 😦


  2. Ola Says:

    Writing my first big data paper, and am becoming quite shocked at the common practices applied to these types of data sets. Most worrying is missing value imputation, which in my limited understanding appears pretty much indistinguishable from data fabrication. We have N=10 for most things, but only N=8 for some, so we’ll just make up the other 2 and now we have a nice clean N=10 for everything and so we can do PCA and clustering and all those other tricks that make pretty figures, but we still don’t really have a fucking clue what it all means. But yay, big data!


  3. drugmonkey Says:

    What does that save the world airline fleet in jet fuel per annum?


  4. Philapodia Says:

    Recently published with a couple of collaborators prior to an upcoming joint R01 submission. Would you, as a wise and benevolent reviewer, care that the investigators on the A0 already have a “established and productive collaboration” and would it affect your score?


  5. Dr Becca Says:

    @Philapodia, in my not-so-experienced opinion, having published together already is a substantially positive thing.


  6. Lee Says:

    Today I’m reminded of the administrative burden that I have to go through just to get a grant to sponsored programs which actually submits the grant. 7-10 business day lead time + 10 approvers…..


  7. anonymous postdoc Says:

    Recently, I’ve been attempting to weigh the relative strengths and weaknesses of becoming an anonymous research assistant professor (frankly a super-postdoc position, no startup, but supporting mentor is moving with lots of startup) at a less fancy-pants institution (though still respectable and good) over remaining an anonymous postdoc at my current MRU (which believes its turds are without odor) with my other mentor.

    If I go, is becoming eligible to apply for R mechanisms really a benefit if I do so from a position of questionable independence? If I stay, what is the strategic value of this institution and situation that makes it worth more than transitioning to even a nominal faculty position elsewhere?


  8. Philapodia Says:

    @Dr. Becca, I would tend to agree but to what extent will it actually help? Hard to measure that, I guess.

    @Anonymous post-doc: Why not look for your own TT position independent of your mentor? You won’t be seen as independent if you follow your mentor to this new Uni, and reviewers will likely ding you for the appearance of submitting your mentors grants as an ESI/NI to get a few extra points. However, if you are away from the mentor then that appearance goes away.


  9. Ass(isstant) Prof Says:

    Still waiting, waiting, waiting for first decision on a manuscript submitted early in December and taking a no news is good news attitude.

    This has been a learning experience over about six months of submissions and presubmission inquiries. The first submission was to a very good society journal with the EIC response: dude, this is really interesting to the assoc. editors and me, but it’s hard to fit it in our scope. Hurry and submit it to a more specialized journal like xxxx. A couple of presubmission inquiries and submissions later, I got the feeling that 1) the paper needed a little tuning for the more clinical audience I was approaching, and 2) lack of BSD-ness might be a disadvantage.


  10. anonymous postdoc Says:


    Oh, I have been! This has been my first cycle on the market – some nibbles, but no bites (i.e. no on campus interviews). I also did not win the K99 lottery, which has definitely impacted my attractiveness to departments. This position would be a bird in the hand, while I try to get at least a few more papers out, hopefully at least one of them high-impact, which I really see as being necessary to be offered a TT interview.


  11. new PI Says:

    I want to know how you find time, as a PI, to think deeply. I’m only in my second year, but fear I have too many projects. I cycle between them, nudging my early trainees along (or make incremental progress on the ones I can’t delegate), but I feel like I’m trying to keep balls in the air rather than finding… a totally new trick that will revolutionize circuses. Or that will at least allow some of the balls to be self-propelling. Metaphor fail. The point is, I’m mentally spread so thin (and feel so behind in publishing) that I don’t think much good can come from this.

    Does this mean I need a small lab? How do others balance the number of projects they’re working on in any given day, week, or month?


  12. Philapodia Says:

    @anonymous postdoc

    “while I try to get at least a few more papers out, hopefully at least one of them high-impact, which I really see as being necessary to be offered a TT interview.”

    Unfortunately while I think good papers are a factor, “funding potential” or bringing your own funding is what a lot of search committees are looking for when deciding their short-list. Without at least some funding history you’re in for a steep uphill climb. If you do take it, focus on getting some money and then move elsewhere when you get a chance.

    @new PI
    Thinking too deeply as a newbie PI gets you in trouble. Publish some good papers (don’t Glamhump!), get grants, and get tenure. Then you can think deeply. Also, make your students/postdocs do some of the intellectual work. They are a resource, so use them so it’s not all on your shoulders.


  13. Emaderton3 Says:

    @anonymous postdoc: I fought the battle as a RAP trying to get funding and lost. Even though I was doing work independent from my mentor (but in her space) on a K25, I was severely criticized in grant proposals from both the NIH and foundation reviewers regarding my independence. After years of trying to explain the situation to my Department, my mentoring committee submitted a letter to them emphasizing my challenges. I was switched to TT (but without any additional resources and not the full probationary period) to make myself more competitive. While I have seen a few RAPs at my institution get R01’s, I think it is an extremely difficult path. However, as others have mentioned, you generally need to have funding in hand to seriously be considered for most TT jobs. And trying to get that funding outside of a K99 as a post-doc is also extremely difficult.


  14. Susan Says:

    Anon postdoc: your top priority should be your own productivity. The move with the smoothest transition for you is the one you should choose. IME search panels look right through “research assistant faculty” — title is meaningless. Also, what is your anticipated timeline of job applications vs. R mech? Between submission, review, revision, resubmission, review, resubmission, review, etc. – the expected value of being able to apply for R mech on your own may be rather low.


  15. Insect Biologist Says:

    Anon postdoc:

    I know four people in my small field who have obtained an R01 grant as a research assistant professor and then found tenure-track positions.

    As an RAP with no desire for a tenure-track position, I’ve been able to support my research by being a co-investigator with my group leader. I was reluctant to submit proposals as the PI because it’s obvious that there is a lot of bias against RAPs. But, I’ve been encouraged by my colleagues to submit my own proposals, and, so far, there have been no conspicuous roadblocks. The reviews of my recent R01 proposal did not mention a lack of independence (although the proposal wasn’t funded), and my NSF program director said I shouldn’t be concerned about my position. So, at least in my field, it appears that RAPs can be viewed as independent and succeed in competing for funding. Perhaps people who have been on the study sections you are considering would be honest about whether RAP = not taken seriously.


  16. Lee Says:

    @Insect Biologist: I’m also an RAP but I’ve never been dinged on NIH applications because of it. At least not on R15/21/03. We’ll see in a few months after this R01 goes in.


  17. Joe Says:

    Every time a reviewer makes some statement about the PI on a grant application not being independent, they get slapped down SRO. This may mean that some reviewers are still scoring with the independence of the PI as a criterion, but you should know that officially, that is not allowed.
    I would try to make it sound like you are as independent as possible. Make sure the facilities page says something about you having exclusive use of certain space, exclusive use of certain office, etc.


  18. Emaderton3 Says:

    @ Joe: I did what you suggested regarding space, office, and even a few pieces of equipment that I had. Then the reviewers just came back saying they were concerned regarding institutional support because I wasn’t on TT.


  19. chemicalbilology Says:

    Noooooo, not SkyMall! My favorite airplane reading material! Where will I shop for pet stairs, a nearly life-size Big Foot statue or the Zombie of Montclair Moors now?


  20. drugmonkey Says:

    apd- take the position that lets you write grants. *however* you need a heart to heart chat with the mentor who is moving about expectations. Is the current mentor looking for someone to run her lab? Trying to bribe someone of your caliber into a 1-2 year transition/lab setup position? Does this mentor just see this as another leg up for you to get a job elsewhere?

    This is important for his/her support letters but also for your ability to write in an independent direction from the start.


  21. drugmonkey Says:


    Occasionally this is from a reviewer thinking they are doing the applicant a favor. Giving you leverage with the Uni. Sometimes itis merely an extra pile-on StockCritique- they just didn’t like the grant and this is not the reason at all. And sometimes you run into jihadists who are never going to budge on this no matter what.

    The answer is the usual one- keep submitting apps!


  22. anonymous postdoc Says:

    Frankly I’m pretty broken up about Skymall too. Although I thought it was odd that they were still selling Sharper Image goods when Sharper Image went out of business years ago.

    Perhaps there’s a metaphor here about Skymall not achieving true independence from its mentors, Sharper Image, Frontgate, and Brookstone…? No?


  23. drugmonkey Says:

    Sharper Image went out of business?


  24. E rook Says:

    @AP: I would not recommend the non-TT faculty position. In my experience, you will be dinged on the K01 applications severely, basically taken out of contention , if they see your salary support is dependent on grants. The lack of start up will mean that older peeps will be on your pubs because you used their equip / space. Most importantly, you will remove yourself from contention, and the clock starts ticking on your eligibility for certain mechs. You can’t get a K99 as a Assistant Adjunct or Research Assistant Prof, and you loose access to travel grants for trainees. The clock starts ticking on eligibility for K01s and others. In my experience, and seeing others, it is a mire that will hold you back. Ultimately, in my experience, having done what you’re proposing to do, I am planning to exit academia after having had several 2 year mechs and 5 r01 submissions. Talk talk talk to other mentors about the situation. You may be better off staying a PD and make your life’s mission for the next 12 months be getting a K99. Though everyone’s experience varies.


  25. toto Says:

    Serious question: what is the stability of these “non-TT faculty positions”? Are they like super-postdocs (i.e. you’ll almost certainly get booted within 5 years), or can you actually expect some kind of career from it?

    More generally, I’m wondering whether American academia has any kind of reasonably stable position for people who want to keep doing research without running a whole “lab” with multiple peons (note: I’m a computational guy / Mountain Dew Chugger, so I don’t have much needs in terms of equipment).


  26. Emaderton3 Says:

    @ drugmonkey: Given how competitive funding has become, I have been told by my mentors that things like TT, your own lab, etc. may just be the things that push other applications ahead of yours even though they should not be considered in scoring (or really even discussed in some cases such as title). After all, if I and other people have equally interesting science, I would imagine the edge will go to the person on TT with a lab and equipment. Believe me, I have been submitting grants to NIH for different R mechanisms, foundations, and societies. One criticism has always been some aspect of my independence and/or institutional support–this has been a constant theme. I realize this may be partially discipline specific, but at least for me it has been a huge issue. I had a R03 that got a decent score with promise with two major criticisms, one of which was TT and the other that I needed to use more cell lines in my experiments (which is fairly trivial). After resubmitting with a letter saying I had been moved to TT, the impact score moved significantly and put me under the payline. Of course, I can’t say it was just because of TT, but that was the one issue that was mentioned consistently in my summary statement.


  27. Dave Says:

    While I have seen a few RAPs at my institution get R01’s, I think it is an extremely difficult path,/i>

    Blanket statements like this are not helpful. This is categorically not true in a lot of med schools where most, if not all, faculty are on the research track, regardless of rank. I have never seen anyone at my place have to deal with criticism about non-TT for R-level grants. It comes up a lot when applying for Ks (institutional commitment), but not Rs. Independence is something that you should have demonstrated as your K25 progressed (that’s the whole point of the mech), and if you didn’t do that, then yes I can see how that would have made things difficult for you down the road.


  28. E rook Says:

    Some people do make careers out of it in my institution. We have distinguished big whigs on our Adjunct faculty roles.. It is rare to succeed but people do, and most people are permanently dependent on others as co-Is, or Core Directors on P-grants; or leading a research project component in a P-grant. You need to be on top of your game from the get-go, offering your services as co-I to as many TT faculty as you can. In the current funding situation, it is difficult to get an R01, and we are told to “drop the ‘adjunct'” label on our titles in the NIH bio sketches, which seems like deliberately misleading the reviewers into thinking your situation is better than it actually is. This is a systemic problem here. You don’t get to make any decisions regarding the direction of the department, you sit at the kids table at the Christmas party, the space is in someone else’s name, and you still have service and teaching requirements for renewing your contract and advancement, but you don’t get paid for it. I sent a long email to my chair detailing the amount of time I’ve donated to the department & university over the years as a way to get a token % effort in case they are audited.


  29. Duke of Neural Says:

    I walked into lab at 10:30 AM to find out that about 10 minutes before, the lab had realized that I contaminated the incubator with fungus and it had wasted a lot of time.

    So I’ve been trying to figure out how to fix that all day.

    But I’m going skiing this weekend, and I got my first result in lab, and the contamination happened weeks ago, so I guess it’s mostly good?


  30. Insect Biologist Says:

    Lee: Thanks for the encouraging information regarding proposal reviews.

    Toto: At my non-med school institution, the stability of RAP positions is marginal, because no funding = no position. For that, and other reasons, working with a really good group leader is absolutely key. For me, being able to pursue my research interests without having to teach or spend large amounts of time on service and administrative tasks outweighs my wish for job security.


  31. Morgan Price Says:

    toto — I’m a research scientist (not a PI) at a national lab, and I think it’s a great job. I’ve been with the same PI for ~10 years and could probably move to another group if necessary so I will likely be here for 25 more. I know a few people with similar jobs at universities, too, either in research institutes or in big well-funded labs. But it might not be possible in less-funded research areas.


  32. Kevin Says:

    Packing up, Moving, and setting up a lab takes up a huge amount of time and is a will lead to a clear loss of productivity. And as the RAP, it will be your responsibility to deal with all that BS. And there’s no guarantee that things will work as well in the new lab.


  33. MoBio Says:

    I heard from a colleague that 900 people applied for HHMI investigator -ships this year.

    Apparently the letters went out to the many 100’s who did not make the first cut…

    This reminded me of how this process went ‘back in the day’.

    Someone I know (who is now quite prominent) was told over the phone that he had been selected as an HHMI investigator. He said (and I quote): “I don’t remember applying” and was told (and I quote): “You don’t apply…we choose”.

    Although HHMI now has a more ‘open’ application process my guess would be that folks are still ‘pre-selected’ to some extent or another.


  34. jmz4 Says:

    Struggling to find a diplomatic way to bring in a new collaborator to whom my boss seems to have taken a disliking. His lab is way more relevant and skilled in the screens that I want to be doing, but my boss insists we stick with our past collaborator for this new project, even though I’ve shopped the idea around with her postdocs and none seemed particularly interested in it (they are in a very different field, but same model organism).
    The lab I want to be working with is a new transfer and is a full professor, while the one I previously worked with is an assistant professor up for tenure this year. My boss seems to think he’s doing her a favor by keeping the projects with her and he seems to see it as a case of male full professor swooping in and poaching exciting projects off of a poor defenseless female assistant professor.
    This neglects the fact that they’re my f-ing projects and I should be able to pursue it with people that are excited about it, not getting partnered with some postdoc who’s only working on it because his boss told him having mammalian collaborative pubs will look good on his CV. Any advice would be appreciated.


  35. Dave Says:

    It is clear to me from this thread that there are a lot of misconceptions about non-TT positions, especially at med schools and similar standalone research centers. No wonder some reviewers are biased against research-track faculty. Sure, it’s not perfect, but it can work and collaboration is very important. There might even be some advantages…..


  36. Dave Says:

    @Duke of Neutral: the very best thing you can do to prevent contamination going forward is get used to working without antibiotics. If you and your lab wean off Pen/Strep in the media, you will have much better control over contamination.

    Oh, and stop using water in your water bath to warm up your media:


  37. E rook Says:

    If you are entirely soft money, how is it justified to spend time writing grants? Is that time donated?


  38. drugmonkey Says:

    Technically illegal. Many Unis have figured out how to cover a nominal effort, 5% at most, on non-Gov funds to get around this.


  39. Grumble Says:

    @new PI: Don’t listen to Philapodia. Your research contributions are only going to be as big as your ideas, so you have to think deeply all the time.

    Perhaps if we all thought a bit deeper before doing an experiment, the constant stream of papers that don’t make any fucking sense would diminish.


  40. drugmonkey Says:

    Papers in my field make sense. Maybe you should switch.


  41. E rook Says:

    I think you could let the deep ideas marinate and put through natural selection by proposing at group meetings and shooting the breeze at lunch. When the time is ripe, they’ll be mature and ready for prime time. Meanwhile you’ve proved your technical muster by conducting good Normal Science (in the Kuhn sense).


  42. Philapodia Says:

    I said don’t thing too deeply, not don’t think deeply at all. Newbies have a short time to prove themselves, and if they get lost in mental masturbation (“I will prove the grand theory of everything!!”) and don’t pull the trigger and get something published they will be out of a job and interviewing at McD’s. Also, reviewers can easily ding newbies in grant applications for great deep ideas for being too ambitious, and you won’t bring home the the IDCs to keep the Deanlets funded. I agree with E rook’s idea that you have to let vertically ascending deep ideas marinate but you have to have horizontal detail work to keep the lights on and get established. Feeding your kids (or self/spouse/dog/cat) should take precedent over trying to become a BSD.


  43. cookingwithsolvents Says:

    Our skymall giraffe TP holder is doing a great job in the guest bathroom.

    Working halfheartedly on finishing a paper after submitting revisions to a different, accepted one earlier today.

    Wondering how many diverse directions a group really CAN make progress on, even if they overlap well in the ‘synergistic’ way….

    Wondering what the best tech/PD/GS ratio is and how to maintain it when PDs don’t have fixed-times in my field (1 yr min, they stay anywhere from 9months-3yrs).


  44. Juan Lopez Says:

    E rook, I used to think like you, but recently I learned that there is no such a thing as donated, weekend, or extra time in NIH funded land. That’s why they say 95% effort, so that if you put 40hrs a week, or 80hrs a week, they still pay you the same.

    The only way is what DM said: you must have hard money for a tiny chunk of your time to maintain the illusion that grant writing, service, teaching, etc do not happen on soft money.

    My mom kept buying all these crap pseudo-medical stuff from Sky mall. She got angry when I pointed out that they are rip offs. I will not miss them.


  45. Emaderton3 Says:

    @Dave: I apologize if I was too broad with my statement. These have been my experiences at my institution (a top 10 NIH dollar medical center). Maybe it is discipline-specific and a bias in the biological sciences. I have heard RAPs on the university-side, specifically engineering, often don’t get institution/independence criticism in their summary statements. Regardless, the title RAP inherently means that you are not “independent” and typically working in and/or dependent on someone else in terms of space, equipment and/or money. When the biggest change I made to a R03 was getting on TT and my impact score skyrocketed 12 points, it makes you wonder. And when my mentors, all tenured and successful, also say it is a problem, then I tend to believe them especially after it has been brought up in every summary statement I have ever received, both from NIH and foundations/societies. I had a grant reviewed last year by one of the largest grant awarding societies, and I received one of the best reviews of my early career. It was reviewed by 2 people, both of which only had 4 comments. The first comment from both reviewers was “it is unclear if the candidate will be switched to tenure-track upon receipt of this award.” In addition, I submitted the same proposal as my R03 for a limited-submission opportunity at my institution. The head of the review committee (who is also an Associate Dean and HHMI investigator) contacted me to let me know I wasn’t chosen. In addition, this person also contacted my Chair and said I would never be competitive for a limited submission opportunity as a RAP. I would think that the science was fairly solid since the R03 resubmission (with the switch to TT) beat the payline. So you can hopefully understand my viewpoint.


  46. Dave Says:

    I am in a very similar environment to you, and I have never heard of such criticisms on R-level grants. The comments you received sound like stock critiques on training/career grants, but you don’t mention the mech. It also sounds like you were screened out by an internal review group at your school for the R03. That is very different. As always, the devil is in the details with your statements.


  47. Emaderton3 Says:

    @ Dave. The criticisms were for R03, R21, and R01 submissions over the last several years as well as two different grants to a large society. In some cases, the science aspects received very positive reviews. I understand the stock critique issue, but the change in scoring on the R03 is interesting. In one R01 submission, I received mostly 2’s and 3’s from every reviewer in all categories. However, one reviewer gave me an unbelievable 6 for Environment which I would think should never occur when someone is at a top institution. I had the necessary collaborators and centers to do the experiments. And believe me, I have written everything in such a way to completely distance myself from my mentor who has not been included on any of these grants nor 2 papers that were published to show my independence. While I agree with you that it probably wasn’t the main issue in some cases, it appears that it did play a factor. Even the PO’s have discussed it with me (“it shouldn’t be relevant, but try to write things more clearly to show your independence”, etc.). I even had a PO suggest that I drop the “R” from “RAP” on my grant title page and biosketch.

    I guess the larger point I was only trying to make was that funding and scores are getting so tight that very small things can set one investigator apart from another, and being a RAP may put someone at a possible disadvantage in some cases.


  48. Dave Says:

    I even had a PO suggest that I drop the “R” from “RAP” on my grant title page and biosketch.

    I think I have raised this before, but I don’t remember what response I got. Would it be dishonest if one dropped any reference to being on the research-track on the biosketch?


  49. E rook Says:

    I was instructed to drop references to less than TT appointments in all biosketches. I think it’s dishonest, but I did it anyway because the competition is. It’s another reason I’ll be glad to wrap up my relationship with this job, too. I know it’s minor but it’s soul draining. It lets the Uni get away with treating you like a red headed step child while keeping up appearances. Everyone does it, though.


  50. Emaderton3 Says:

    @ Dave and E rook. I wasn’t comfortable dropping it. It is also something a quick Google search can expose.

    More importantly, where am I going to buy the Bigfoot statue for my yard now???

    (P.S. Why don’t the “notify me” options actually notify me?)


  51. Philapodia Says:

    @Dave “Would it be dishonest if one dropped any reference to being on the research-track on the biosketch?”

    @Emaderton3″I wasn’t comfortable dropping it. It is also something a quick Google search can expose.”

    @ E rook “I was instructed to drop references to less than TT appointments in all biosketches. I think it’s dishonest, but I did it anyway because the competition is.”

    Why is not stating that you’re not a TT faculty member dishonest? There isn’t any requirement to be TT for most NIH awards, just that you have the skills and setup to do the research. Here’s the language from PA-13-302 :

    “Any individual(s) with the skills, knowledge, and resources necessary to carry out the proposed research as the Program Director(s)/Principal Investigator(s) (PD(s)/PI(s)) is invited to work with his/her organization to develop an application for support.”

    The whole “you’re not TT so you’re not as good as us” crapola is just reviewer bias. By not putting a “Research” in front of your “Assistant Professor” title (which is the prerogative of your institution), you remove that bias from the reviewers and they can focus on the merits of the proposal. You’re actually helping them be better reviewers by taking that criticism from them. If they get pissy about if after google searching you (who has time to do that anyway?? I don’t, nor would I care!), then you may want to find a different study section with more enlightened reviewers.

    DM, what happened to the math problems? They made me feel smart.


  52. E rook Says:

    By that logic, Why stop stop at dropping the R, and dropping the A, too?


  53. Philapodia Says:

    Sure, why not? There isn’t a rank requirement either. Your record should be what you’re judged on, not a title. Again, it’s reviewer bias and not NIH policy that’s driving this issue.


  54. Emaderton3 Says:

    @ Philapodia: In a perfect world, rank shouldn’t matter. I was actually saying that the suggestion was to drop the “R” from RAP to give the false impression that I was an Assistant Professor which would also imply TT.

    If I have to help a reviewer be a better reviewer, than maybe he/she shouldn’t be a reviewer.

    I do agree it is bias, but I am not sure how to get it out of the system. In my case, it affected their view of institutional support that I wasn’t TT.


  55. Philapodia Says:

    Again, TT isn’t a requirement for R funding, although a lot of reviewers assume that it is. It’s the same with preliminary data for R21’s which isn’t required officially but many reviewers seem to think is.

    “If I have to help a reviewer be a better reviewer, than maybe he/she shouldn’t be a reviewer. ”

    You want to get funded, right? Grants are simply a sales document meant to convince reviewers (i.e. consumers) that they should buy your science. If it’s true and helps sell your product, use it! Kind of a moot point now that you’re on TT, but still true.

    How to get it out of the system: “Be the change you want to see in the world” – Ghandi
    Alternatively, pull a Tonya Harding on them as they exit CSR…


  56. drugmonkey Says:

    I believe my institutional pre-award folks in the grants office recommend deleting any reference to non-tenure track faculty appointments on Biosketches. I also cannot once recall anyone fighting at study section over a title listed as merely “Assistant Professor” when this was non-TT.

    In my experience, fights over the true independence of the PI have little to do with the job title and much more to do with the publication record and presence/lack of a clear message describing the PIs independent program within a longstanding collaboration with a BigWig.


  57. anonymous Says:

    Challenging time and adversity don’t last forever !!!.


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