Phenomenal science powers!

So you toil for 4+ years in graduate school, 4+ years as a post-doc, land your first academic gig. Now you get to do all this awesome science, right? Well, sorta…

Oy! 10,000 years in the cave of graduate school will give you SUCH a crook in the neck!

Oy! 10,000 years in the cave of graduate school will give you SUCH a crook in the neck!

A Fine Trip Spoiled

I had a dream the other night that inspired this comic. My dream was about waiting for a connecting flight. I decided to take it easy and do something fun, then realized that my flight was leaving soon and I was nowhere near the gate. Then I got on a train and realized I was going the wrong direction. Anyway, I woke up to the realization that I’d relaxed and done fun stuff most of the weekend (I did work some in the evenings) and that I had an unfinished grant that was still due this week. As it turned out I finished up my grant quite nicely despite the slacking off- or maybe even because of the slacking off. But it gave me the inspiration for this comic.

You see, writing and submitting a grant proposal is a lot like planning for a vacation that you’ll probably never get to take. The work you’re proposing should be fun and interesting (otherwise, why are you trying to get money to do it, right?) but your chances are pretty slim that you’ll ever get to do it- at least in the form that you propose it. I’ve started to think of the grant process as a long game (see this post from one DrugMonkey)- one where the act of writing a single grant is mainly just positioning for the next grant you’ll write down the line. Writing grants give you opportunity to come up with ideas, to consolidate your thoughts, and think through the science that you want to do and how you want to do it. The process can push you to publish your work so that you can cite it as preliminary data. And it can forge long-lasting collaborations that go beyond failed proposals (though funded proposals certainly help to cement these relationships in a much more sure way).

I think “A Fine Trip Spoiled” may be the title of my autobiography when I get rich and famous.


New biosketch format for NIH

Just got word of this from the Twitters- the NIH is announcing rollout of a new biosketch format for grant applications. I thought I’d summarize the information about it here to make things easy.

  1. Starting for grants that would be funded in 2016 (so anything you apply for in 2015 will have this, essentially)
  2. Will be a five page limit (as opposed to 2 page for current format)
  3. Will NOT include a ‘bare’ list of 15 publications
  4. Now includes a new list of up to 5 of your “contributions to science”, which can include up to 4 citations each (your own presumably). So that’s a total of 20 citations you can have.
  5. You will be able to include a link to your full citation list in an online database (NIH resources sciENcv or My Bibliography are mentioned but could be others I guess)
  6. Here’s a template that includes an example new biosketch
  7. More information can be found in the announcement here from the NIH on Salley Rockey’s blog
  8. As it’s being rolled out the requirement for the new format will be stated in the RFA – SO LOOK FOR THIS IN ALL RFAs from here out. Two pilots already have it RFA-CA-13-501 and  RFA-CA-13-502

The upsides: In my opinion the addition of the contributions to science will be the biggest one and should allow you to really highlight your publications (or lack thereof) in appropriate context. Plus space for moar buzzwords!

The downsides: It’s gonna be a pain to write (like a mini grant in there) and reviewers won’t read this one either.

I dream of science

I had a dream last night- after yesterday hearing about possible furloughs at the lab due to the government shutdown. Here it is:

I was trying to go into a building and needed to go through security. Now that I think of it, it had a lot of similarities with the NIH campus main entrance. I needed to talk to a security guard so I put my bag down. After he asked me what I did- that is, what I studied, I was surprised to find that he was a scientist too. We had an interesting conversation about science. Then I turned around to get my bag (presumably to enter the building). However, I found that someone had completely taken apart my 35 mm camera while my back was turned- it was entirely in pieces, even the lens was just a pile of glass and black metal and plastic parts. I was shocked, angry, and despondent all at the same time.

I’ve been thinking about this dream all day and it seems to sum up my career stage, my concerns about making it to the next step and succeeding in science, and my concern over the state of science in the US currently- especially during the shutdown. Imagine that the camera represents my vision of science and security represents the grant/career process, especially with an emphasis on funding organizations. Also the security guard? An alternate ending to the career story. The mind is a wonderful and terrible place when it’s worried about something.

Goodbye to two good friends

(Note: this post isn’t nearly as sad as it might seem from the title or the introduction below)

Yesterday I lost two close friends. We had been friends for five years, though our relationships had extended a tumultuous 10 or so months before that. Given that we still have unfinished business I expect our friendships to straggle on a little longer. But really, it’s over. My friends have helped me grow in a number of important ways- become more mature, deal with different personalities, forced me to communicate more clearly and to take criticism in a constructive light. The friendships both challenged me in different ways and supported me through a fragile time in my life. I will miss both of these friends for some different reasons- and some of the same reasons.

Like many friendships they have ended because of what other people thought about them. A small number of people had comments on our friendship- some of the comments, upon reflection, were probably well-placed, others certainly were not. But that outside influence is what really broke us apart. I hope that we can become friends again in the future- but we both will have changed so much in the intervening time that we may well be unrecognizable to each other. Still it would be nice to continue this friendship.

Bye Bye

Farewell Systems Biology of Enteropathogens and Systems Virology Centers – you will be missed but not forgotten.

Here are a few mementos of our time together….

  1. Ansong C, Schrimpe-Rutledge AC, MitchellH, Chauhan S,Jones MB, Kim Y-M, McAteerK, Deatherage B, Dubois JL, Brewer HM, Frank BC, McDermottJE, Metz TO, Peterson SN, Motin VL, Adkins JN. A multi-omic systems approach to elucidating Yersinia virulence mechanisms.Molecular Biosystems 2012. In press.
  2. McDermott JE, Corley C, Rasmussen AL, Diamond DL, Katze MG, Waters KM: Using network analysis to identify therapeutic targets from global proteomics dataBMC systems biology 2012, 6:28.
  3. Yoon H, Ansong C, McDermott JE, Gritsenko M, Smith RD, Heffron F, Adkins JN: Systems analysis of multiple regulator perturbations allows discovery of virulence factors in SalmonellaBMC systems biology 2011, 5:100.
  4. Niemann GS, Brown RN, Gustin JK, Stufkens A, Shaikh-Kidwai AS, Li J, McDermott JE, Brewer HM, Schepmoes A, Smith RD et alDiscovery of novel secreted virulence factors from Salmonella enterica serovar Typhimurium by proteomic analysis of culture supernatantsInfect Immun 2011, 79(1):33-43.
  5. McDermott JE, Yoon H, Nakayasu ES, Metz TO, Hyduke DR, Kidwai AS, Palsson BO, Adkins JN, Heffron F: Technologies and approaches to elucidate and model the virulence program of salmonellaFront Microbiol 2011, 2:121.
  6. McDermott JE, Shankaran H, Eisfeld AJ, Belisle SE, Neumann G, Li C, McWeeney SK, Sabourin CL, Kawaoka Y, Katze MG et alConserved host response to highly pathogenic avian influenza virus infection in human cell culture, mouse and macaque model systemsBMC systems biology 2011, 5(1):190.
  7. McDermott JE, Corrigan A, Peterson E, Oehmen C, Niemann G, Cambronne ED, Sharp D, Adkins JN, Samudrala R, Heffron F: Computational prediction of type III and IV secreted effectors in gram-negative bacteriaInfect Immun 2011, 79(1):23-32.
  8. McDermott JE, Archuleta M, Thrall BD, Adkins JN, Waters KM: Controlling the response: predictive modeling of a highly central, pathogen-targeted core response module in macrophage activationPLoS ONE 2011, 6(2):e14673.
  9. Aderem A, Adkins JN, Ansong C, Galagan J, Kaiser S, Korth MJ, Law GL, McDermott JG, Proll SC, Rosenberger C et alA systems biology approach to infectious disease research: innovating the pathogen-host research paradigmMBio 2011, 2(1):e00325-00310.
  10. Buchko GW, Niemann G, Baker ES, Belov ME, Heffron F, Adkins JN, McDermott JE (2011). A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteinsMolecular Biosystems. 6(12):2448-58.
  11. Lawrence PK, Kittichotirat W, Bumgarner RE, McDermott JE, Herndon DR, Knowles DP, Srikumaran S: Genome sequences of Mannheimia haemolytica serotype A2: ovine and bovine isolatesJ Bacteriol 2010, 192(4):1167-1168
  12. Yoon H, McDermott JE, Porwollik S, McClelland M, Heffron F: Coordinated regulation of virulence during systemic infection of Salmonella enterica serovar TyphimuriumPLoS Pathog 2009, 5(2):e1000306.
  13. *Taylor RC, Singhal M, Weller J, Khoshnevis S, Shi L, McDermott J: A network inference workflow applied to virulence-related processes in Salmonella typhimuriumAnnals of the New York Academy of Sciences 2009, 1158:143-158.
  14. *Shi L, Chowdhury SM, Smallwood HS, Yoon H, Mottaz-Brewer HM, Norbeck AD, McDermott JE, Clauss TRW, Heffron F, Smith RD, and Adkins JN. Proteomic Investigation of the Time Course Responses of RAW 264.7 Macrophages to Salmonella Infection. Infection and Immunity 2009, 77(8):3227-33.
  15. *Shi L, Ansong C, Smallwood H, Rommereim L, McDermott JE, Brewer HM, Norbeck AD, Taylor RC, Gustin JK, Heffron F, Smith RD, Adkins JN. Proteome of Salmonella Enterica Serotype Typhimurium Grown in a Low Mg/pH Medium. J Proteomics Bioinform. 2009; 2:388-397.
  16. *Samudrala R, Heffron F, McDermott JE: Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systemsPLoS Pathog 2009, 5(4):e1000375.
  17. *McDermott JE, Taylor RC, Yoon H, Heffron F: Bottlenecks and hubs in inferred networks are important for virulence in Salmonella typhimuriumJ Comput Biol 2009, 16(2):169-180.
  18. *Ansong C, Yoon H, Norbeck AD, Gustin JK, McDermott JE, Mottaz HM, Rue J, Adkins JN, Heffron F, Smith RD: Proteomics Analysis of the Causative Agent of Typhoid FeverJ Proteome Res 2008.

*these were really from slightly before our time- but I’ll count them there anyway

The 5 stages of reading reviews

In many parts of our lives we have to receive criticism. Sometimes directly, from someone like a boss telling us we screwed up, and sometimes indirectly, in the form of written reviews from anonymous reviewers. In science, reception of criticism, ingestion, and self-improvement as a result are a part of the gig. A BIG part of the gig. We submit papers that get reviewed (that is, criticized) by at least two peer reviewers. We submit grant proposals that get shot down. We present ideas that rub somebody the wrong way- so they tell us in public ways. I’ve had a lot of experience at this. A lot.

Today I found that the renewal of a collaborator’s 30 year old NIH R01 (it’s been renewed 6 times before) that I wrangled myself a co-PI spot on was not discussed in study section. This happens when it gets scored poorly by reviewers and so doesn’t move to the stage of open discussion when the group of reviewers meets. It means that the grant will not be funded and generally that it didn’t make the top 50% of proposals for that round. It stinks.

Here’s how I often react (riffing off of the 5 stages of grief):

  1. Denial. When I first get a poor grant review I often think, “hmmm… that’s weird, there must have been some kind of mistake. I’ll talk to the program officer and get this all cleared up right away”. Loosely translated this means, “my proposal is so good there’s no possible way it could have been not discussed in study section so the only reasonable explanation is that there was a terrible, and highly unlikely, clerical error.” Yeah. Right.
  2. Anger. “Those STUPID nitwits! How could they be sooooo stupid as to not see the brilliance of my obviously brilliant study? What total imbeciles. It’s a good thing that it’s all their fault.”
  3. Bargaining. “OK. You know what, I’ll do better. I’ll do better and write better and experiment better and this will all go away. It has to, right?”
  4. Depression. “I’m a failure and nobody likes me. Also, I can’t do science and I’m an imposter. Everyone else is way smarter than I am. Holy crap what am I going to do with myself now?”
  5. Acceptance. “Right. So I see the points that I need to fix. And I recognize the points that the reviewers just didn’t get. Since they didn’t get them it means that I didn’t communicate them well enough. I can fix this.”

Of course, getting through these to stage 5 is the goal. That’s where the rubber meets the road. How do I take what someone else has criticized me on, strip away the emotional attachment (they’re no attacking me), triage the good from the bad (face it, sometimes reviewers are not paying attention), and apply what you’ve learned to improve what you’ve produced. This process, and the uncomfortable stages that accompany it, has led me to write papers, improved the papers I’ve already written, spawned new ideas, and promoted self realization and betterment. Learning from how others see you is a critical and under-appreciated skill.


Upside/Downside: Getting a grant rejected

So I’m starting a new feature to talk about the things related to my professional career that I’m ambivalent about. This is for my millions of followers/subscribers who might be interested in this kind of thing.

Receiving a rejection for a grant proposal


So part of what I do is writing applications for funding to send off to various funding agencies (e.g. NIH, DOE, etc.). These proposals are reviewed by a panel of my peers- evaluated for quality, innovation, impact, and how well they fit the goals of the request for proposals that I’m answering. A standard NIH R01 grant runs 12 pages and takes several months of preparation and work to assemble and get perfect- it generally involves a lot of personal investment; time, effort, emotional attachment.  In this funding environment (very poor) they have a high probability of being rejected. The reasons vary but the effect is the same. No money, no 3-5 years of guaranteed support, no boost to the ego for having your peers recognize your brilliance, no accolades of any kind.

Your grant has been rejected. You may or may not have the possibility of responding to reviewers’ concerns and resubmitting a revised version of the same grant. It’s the end of the world. Or is it?


  • You don’t get the money. That sucks.
  • You won’t have support to pursue that really cool plan that you’ve agonized over for so long.
  • You won’t get the ego boost that comes from success. In fact, the opposite. You have a big kick in the pants from the reviewers and the funding agency telling you that you didn’t make the cut. That sucks too.
  • The reviewers saw major flaws in some part of your proposal, or you didn’t sell it well enough. In either case, you need to take this to heart seriously.


  • You’ve spent a good deal of time seriously thinking about this research project. That counts for something. Really. Now you have a plan of action. If you are lucky enough to have some kind of funding to get some part of this done then you now know what 7395256948_e355c85bc3_bto do.
  • These kinds of efforts are very good at highlighting where you need more preliminary data. Maybe you can figure out a way to get some of that accomplished to provide preliminary data for the next round.
  • You now should have a set of good suggestions about where you need to improve and generally, if you read between the lines, you can figure out where your sales pitch has gone wrong and you haven’t made yourself clear.
  • Writing up the background and significance for a grant and gathering all the references necessary is approximately equivalent to writing a review article. Make it one. I’ve done this successfully in several situations.
  • You now have an additional corpus of text, ideas, and figures to recycle for the next grant proposal. And you should do this as much as possible.


So, in summary. If you’re in the sciences get used to rejection. A lot of rejection. Come to embrace it, accept it, and love it (OK, maybe not love it) and your life will be considerably less stressful. The simple truth is that a lot of people have a lot of great ideas. If the idea is really good it will persist and grow better with time and revisions. Hopefully someday it will land you a big bunch of dough. I know I’m still holding out that hope.