Continuing fallout

Still trying to process ongoing sexual harassment allegations of the last few weeks. At the time I wrote my last post, I don’t believe that this post from Kathleen Raven had been posted. Kathleen describes two stories of harassment and abuse- first at the hands of a high school teacher/coach, and then a lengthier story of her interactions with Bora Zivkovic.

Much has been written in the science blogosphere about that second bit ( it has even hit Nature)- but for some reason it was actually reading the first part of her post that made me feel as though I really wanted to cry. I did, in fact, sit in my office and cry. I cried for the vulnerability of all teenage (and younger) girls, who, with fragile confidence and little real world perspective look for external validation of their talents, gifts and abilities from people who seem to know more. There is always some person (a man usually) there in a position of power- a teacher, a coach, a family friend, willing to use that vulnerability to suit their own needs.

And in your innocence and inexperience- you don’t know enough to think they are creepy- because they tell you they are your friend, they are looking out for you, and you are special. You crave that validation of your fragile teenage self confidence, and you trust in the essential goodness of people. It is crushing to realize that they just needed you to satisfy their desires- and that the attention they paid to you had nothing to do with who you are- other than the fact that you possess a vagina along with 50% of the general population. It is humiliating to feel like you should have known better. There is overwhelming sadness too- to feel like you lost someone you loved- even though you don’t  understand yet what real love between equals looks like…. and this definitely wasn’t it. You stay silent, not because you are OK, but because there was real damage.

I was once this girl, and I now have two daughters at this vulnerable age. What happens to my daughters at the hands of boys at school, of teachers and coaches at school, of boys they meet in college, keeps me up at night. On one hand you don’t want your children to know the ugliness of the world because you want to protect them. On the other hand, you cannot protect them and that it is essential that they know the ugliness of the world so they can protect themselves. You work against the backdrop of a less-than-enlightened culture reflected in the school system- where girls are blatantly taught that they should ‘dress modestly to avoid being distracting’ to the boys. Where there is no official lesson teaching the boys that it is their own responsibility to control themselves- that girls are not objects to be leered at or used, and that these boys need to keep their eyes on their paper. When are we going to teach boys that they are fully responsible for their own actions?

These boys eventually become men. Men who mysteriously got the message that women are objects to be used to satisfy their desires, whatever those may be. Men that learned in their youth that they either can’t or don’t need to control themselves because someone else is responsible for that…… and the cycle repeats itself for life.


Stay within the lines. The lines are your friends.

Starting this post by saying:

1. I stand with DNLee.

Everyone who has been watching the science blogosphere in the last week knows what that means. Everything that happened to Dr. Lee from Ofek to how the removal of her post was handled, to excuses that were made for this and that……was a big snowballing shit load of wrong. I’m so sorry that Dr. Lee was victimized.

2. I stand with Monica Byrne, Hannah Waters, and every woman who has been the target of sexual remarks, harassment, or abuse in the workplace. That, as should be apparent by now, pretty much includes everyone who goes to work bearing two X chromosomes. The end results of this kind of thing are never good- they damage the victim (you can read the two posts above, or maybe talk to your own wife or daughter about how this hurts if you still don’t get it) and also have consequences for the perpetrator sometimes.

Honestly, I feel kind of shell-shocked from watching all of this unfold.  I’ve read all the posts, at least as many as I could find particularly regarding the business of men making sexual remarks to women at work, or where a professional power differential exists. Sometimes it is just really hard for me to believe that in this day and age, some men could be so fucking clueless. Its not like this is the first time you have encountered a girl in the workplace y’all. (and no, I don’t want to paint you with a broad brush, because I know and work with some really professional guys)

This morning Seth Mnookin has another post about this at PLoS Blogs….in which, I think, he tries to take a bold step of saying let’s DO something about this problem right NOW. Seth comments thusly:

One obvious step is to insist that there be consequences for people who engage in inappropriate behavior regardless of whether they were aware that their behavior made someone uncomfortable at the time.

I’m on board with that, but many of the commenters on Seth’s post were not. Commenter NIkita said:

I think I may be missing something, but could you please clarify where Bora acknowledged that he “sexually harassed” Ms Byrne? Could you also cite evidence of Bora harassing Ms. Byrne? So far I have only seen that Ms. Byrne was offended over a misunderstanding. I see no evidence of sexual harassment. (bold is mine)


You are looking for heads to roll for Bora, an innocent individual who’s only mistake seems to have been that he misunderstood context of a conversation and opened up to a stranger without any intent to offend or harass.

and Bruce K. says:

This person cannot even articulate what the other person did wrong and you say he must be punished for it, EVEN if he did not know he was doing anything wrong?

and Tom B. says:

I’m not condoning his behaviour, just simply noting that as Nikita points out it seems to be the result of a miscommunication between people with different boundaries,

I can’t read any further down in the comments because I can’t take any more of the same tired argument. I don’t give a rats ass about people’s intentions. I really don’t. Isn’t there some saying about the road to hell being paved with them …. Let’s get one thing straight: Talking about strip clubs and your sex life with a woman in a professional setting is NEVER a ‘misunderstanding’ a ‘miscommunication’. Do you even understand how offensive it is to suggest that the victim was so stupid that she ‘misunderstood’ the perpetrator’s intentions????? Don’t even try to mansplain that away.  If I came home from work and told my better 1/2 that some guy I work with was telling me about his trip to the strip club and about his sex life, I’m pretty sure DrMrA would not think that was a ‘misunderstanding’ or a ‘miscommunication’.

And the second trope that always follows this one is the ol’: does this mean we can’t flirt with anyone at work, does this mean that we can’t hug anyone at work, does this mean that we can’t ever look our female colleagues in the eye for fear we will be accused of harrassment, …. we don’t know where the boundaries are. Oh noes!

On this one too, I say- give me a fucking break already. This is NOT mysterious. It just isn’t.  Implying that you guys can’t figure out where the lines are is to make you appear as the vicitim, and insult all of our collective intelligence. I’m so tired of fighting this. Just tired.

So let me lay it out there for you, so you know where the lines are:

1. Do not, under ANY circumstances, make ANY remarks to your female colleagues of a sexual nature. No jokes. No comments. No analogies. None. ZERO.

2. Do not, under ANY circumstances, make ANY remarks to your female colleagues regarding their anatomy. None. ZERO.

3. The ‘good intentions’ defense will NOT excuse you if you disobey #1 and #2.

4. School your colleagues, your friends, and your sons in this.

THAT, is all.

P.S. Another post appeared about this at Slate, while I was putting together this post.


Don’t you ever just sit at your desk mentally counting the virtual mountain of tasks that have  to be completed and feel totally overwhelmed? I’m totally there.

Yes, this post is going to be a confession of sorts, but I’m fully aware that my life isn’t unique and each of you probably have a similar mountain to the one I’m looking at right now. I am in the middle of producing 2 R01s, which, in itself is a crazy thing to attempt. I feel like I’m banging my head against both of them, never really making the kind of progress that needs to be made. The first is a resubmission, got a score (a bad one), but I’m having trouble seeing how to make the re-write work. At the same time, the initial application got scored so I feel like I MUST resubmit.

The second is a new submission of a project that I am infatuated with- but the needed techniques are going to be somewhat outside my comfort zone- so that is a challenge as well. Anyway, I’ve got study section between the two R01 deadlines, so there are a few (not to terribly many) grants to read for that. One of my trainees has two grants of her own with deadlines in the middle of all of this, for which LORs and such are needed.. and I have one paper accepted (a little good news is *so exciting*) with minor revisions- and so someone has to do those as well. Several manuscripts in various states of preparation await my attention.  I also have a talk (also good news, right?) at an important meeting for my field immediately following the second R01 deadline. Then I applied for a leadership training in my institution- and attendance is mandatory- 1 day each week for 6 weeks- to begin around the time of the meeting.

Yesterday I discovered that I can’t get back from my meeting talk in time for one of those sessions- so that training has to get put off until next year. Spent part of my evening last night trying to sort out how to make this work so I could do both- but short of me spending an entire night in the air and coming directly to training 24 hours sleepless… it is not going to work. Disappointing because I feel I really want some formal training in this area, because it will help me with potential next steps in my career. At the same time, this is just the way it has to be.

And finally, just before bedtime last night I opened my email to find my kid-sitter quit.  I found myself worrying about in lieu of sleeping last night.  I find myself scrambling to figure out how we are going to cover the kid-shuttling duties in the midst of all these other tasks…Heavy sigh… I totally thought I had that one in the bag….

One year ago some life events made me promise myself I’d be more purposeful about what I chose to do and not to do. I am not feeling good at that right now… and the days go by….

Cell, Science, Nature…. and… eLife?

My better half returned from his travels yesterday with some interesting nuggets of information he learned on his trip. Among those was this:


Wow. Consider me informed. As the new guy in the OA slate of journals… eLife wants your:

“outstanding research in the life sciences and biomedicine, which ranges from the most fundamental and theoretical work, through to translational, applied, and clinical research.”

HHMI, Max Planck and Wellcome are funding this effort, and as of now publishing in eLife is free for a while, and content is open access – an improvement over S/C/N.  The editorial leadership is very strong, led by EIC Randy Schekman, even if a little XY heavy ( only 5/21 senior editors are women – just sayin’). The editorial leadership of all working scientists appears to look at every submitted manuscript and determine its suitability for peer-review- as opposed to those other single word journals that use professional editors who are not working scientists determine the impact of your work (for starters). Haven’t we all complained about that at one time or another?

Emphasis in the peer review process at eLife seems to be on rigor, brevity, and generally less painful review/revision process.. and they have a nifty little video (sorry WP won’t let me embed) about their review process:

eLife: Changing the review process from eLife on Vimeo.

Oh how I have longed for concise guidance on revisions, for limiting revisions to those that are essential to the point of the paper, and for limited rounds of review. Is it too good to be true that you could get a paper into a very selective journal in less than the two years it takes you to do three pages of additional experiments that may or may not be relevant to the conclusion of the paper?

Decisions and responses for manuscripts accepted to eLife are published with the published article (with the author’s OK). And…they keep track of the mean time for submission to acceptance on their homepage… which is info that many journals don’t share (Cell, for example- publishes their mean time from submission to first decision as 21 days… but you could still go through a year of painful revisions after that).

Could eLife be the open access answer to the glamormagz? Maybe. They certainly set themselves up that way. I only learned about this yesterday (and judging by the papers published in eLife from my field (only 23 so far), not many of my colleagues know about it either)… but I’m interested to see how this journal will evolve. I’m reading this little gem with interest right now.

Impact Factor Warz… again.

I’ve not been blogging or reading too much blog recently. Late last week, in what started as an attempt at cleaning up my blogroll, I rambled on over to Isis place, electronically of course. Seems that esteemed physiologist Isis and open access pioneer Michael Eisen had a bit of a falling out over whether or not one should forgo potential publication in teh glamormagz, and go on the perceived moral high ground to an open access journal instead. I’m pretty sure you know which side Michael Eisen was on…. and as for Isis , she’s got a higher moral high ground.

Larger than the Open Access warz, I feel that I have a moral responsibility to increase the access to science careers for women and minorities. I can’t hold the door open for those folks unless I am standing on the other side of it.

Yeah, although I am not a minority so I don’t have the same perspective as Isis, as a girl with white guys on both sides, I understand at least that part of the sentiment. I really do. But what I don’t quite get- is why the OA-high ground and the increase-of-our-kind-in-STEM-disciplines high ground have to be pitted against each other.

It has been argued by Isis and many others in the comments that glamormagz pubs are essential for advancement in academic science, and I guess I think that interpretation is pretty rigid, at least in my admittedly (but I have gone through tenure, am on P&T, and on numerous hiring committees) limited experience. Why? Because I don’t think that single word journal pubs are necessary for promotion and tenure everywhere. Not every academic institution in this country has the same view of this as Harvard, Stanford, or Berkley. In fact, for the most part, if you have $$$, and a reasonable quality and number of papers as defined by your institution, and you have made an impact on your field that is defined in the letters of your tenure packet (which will be written by experts in your field who should know what your important contributions in your field are above just calling them S/C/N papers), you have done a respectable job at teaching and you have the support of your department members and chair- I don’t know why you wouldn’t get tenure. Despite what Dr. Becca says here….

 If you are a person at any pre-tenure stage of an academic career (incl grad students & post-docs), the reality is that you are judged by a finite number of things: 1) where you did your PhD; 2) who you do your post-doc work with; and 3) the IF of the journals you publish in.

That is not my experience on P&T decisions. Not.even.close.  P&T committees work really hard to try to incorporate lots of factors into the tenure decisions- but it would be foolish not to know that grants funded trumps every item on that list above. (I’m sure someone is going to scream that you need S/C/N papers to get $$, but what are you gonna do)

Nor do I think that the IF of the journal means anything about the impact of your paper published in that journal (as was wisely pointed out by Mr. Gunn in the comments of a follow up post by Dr. Becca).  It seems to me pretty stupid (or just lazy) on the part of a P&T committee to give more weight to a paper published in IF 30 journal, that has been cited 3 times total in 5 years, than to the paradigm shifting paper in the IF 4 society journal that has been cited 500 times in 5 years.  I’ll just note that the identification of Helicobacter Pylori as the causative agent of peptic ulcers was published in a journal none of you would recognize (with an an IF at the time of probably <2 if the trend on ResearchGate is correct, anybody know the IF of the Medical Journal of Australia in the 1980s?). Those guys singlehandedly changed the treatment for that disease and associated conditions, impacting millions of people and winning the Nobel prize in the process. I hope you are not saying that because their findings didn’t appear in S/C/N pub they didn’t have impact? If that is how academic science is today, well, it is pretty (earmuffs) fucked up.

Give the P&T committee as much quantifiable information about the impact of your work as possible, and don’t just rely on journal IF. Set yourself up an account on Google scholar and see precisely how many times each of your papers has been cited in the academic literature. You should include this information in your tenure packet on the citation for each of your papers, highlighted in bold. If it were me, I’d include OA statistics as well on the papers you have published in OA journals – like downloads for example, because I don’t think that there is any one perfect measure of impact and I’m unwilling to settle for any single imperfect measure. Choose the list of people in your sub-field who you will suggest to the chair (when he asks) as your external reviewers with extreme care, talk to some of your trusted colleagues for ideas if necessary. Find someone who lives in the 21st century academia who knows how to do this and can help you be proactive in the preparation of your tenure packet.

Speaking from personal experience, it takes some balls to go OA whole hog. Even after tenure (because you have trainees relying on pubs for future jobs, and it feels like gambling with their futures to go OA all the way). So I try not to vilify others for their choices in this area- but instead I try to make small inroads where I can. I stopped reviewing manuscripts for non-OA journals, I bring up OA whenever I can at my academic society (and with their journals people), I’ve put some of our data into OA journals… and I don’t even utter the word Elsevier unless it is preceded by the words ‘the evil’ .

And now, back to our normally scheduled grant revising program. uuugh.

Working hours

My kids are in school, DrMrA is out knocking everybody’s socks off at a conference, and I’ll be working in my office working on a response to a grant review. Which brings me to something I’m mulling over today- how much, or how little, actual working we expect from our laboratory staff (trainees, techs etc). Seems timely, what with it being Labor day and all.

Here is every PIs basic problem- how do we get absolutely the most (and most reliable) data out of each individual that we pay to work in our labs? I think we should get THE MAXIMUM of correctly done, well controlled work. I say this because for the most part we are spending taxpayer dollars for trainees’ salaries, and taxpayer dollars for our experiments.

Over the years I’ve seen the entire spectrum of PI personnel management techniques- from the  ‘accept-that-I-expect-you-to-be-chained-to-the-bench-during-thy-training-here’ approach all the way to the ‘however-long-it-takes-you-to-get-the-data-is fine’ approach (OK, big fat lie- I’ve never seen that second one- but some milder permutation marked by excessive patience). I’m sure you all know at least 1 PI who wants to abolish holiday breaks (and every other break) and feels that time to tend your personal life is a little luxury you can’t afford in the cutthroat world of academic science. There are those that think that if you are not working doing experiments at the bench, you are not working. For these PIs, more time = more data. This approach is only a strategy for coaching the team you have available, and I’m not sure I’ve ever seen it work very well.

In my little universe this issue isn’t about time served in data production, it is all about motivation.  I may seem like I’m kind of a softie- I don’t count people’s hours, and I don’t really think about it when someone asks me if they can take some time off to take care of this or that (unless it is a repeated pattern). I don’t want to chain trainees to the bench (figuratively). But I’m a tough-ass certain ways-  I don’t want personnel in the lab that aren’t internally motivated to be absolutely excellent.  I can’t teach a trainee to love science, and I think it would be silly to force someone to work on a problem that I find intellectually thrilling. I want personnel that are driven to know the answers to the questions we are asking. It is frigging hard to be an academic scientist right now- and I want those that step up to that challenge, by working harder, by reading more, by thinking more creatively, by writing and presenting better. I’ll go one step farther and say we shouldn’t be training any people in academic science who don’t have these qualities- and I’ve seen many who don’t. I prefer a strategy that emphasizes starting with the right players.

I’ll do my part too- I will freely give trainees in this category all my hard earned knowledge, both from life and from the academic-school-of-hard-knocks. Us PIs and our trainees have to realize that our fates are intertwined- the ability to keep the $$ rolling in for projects we care about and said trainees’ stipends, tuition and supplies, depends fairly directly on the ability of those trainees to produce data and thus, papers.

Victory Dance

Sometimes you have to do one.

Right now, as the academic science world is undergoing its own little armageddon…..grant getting is just shit as the funding line is in free fall, people are dropping from the field like flies, and jobs are non-existent….. and all that can seriously get a mid-career academic scientist down.

But, on the other hand… we have two manuscripts (that I totally dig) well on the way to acceptance, two trainees that are on FIRE (not literally, in a good way). We have two R01s in prep for which I’ve decided to solicit the most honest and brutal feedback- and my colleagues have totally stepped up for that.

Yeah, I know – the big picture is still the same- but we have to focus on these little milestones when we can.

On representation at meetings…CSHL Microbial Pathogenesis 2013

To take a page from Jonathan Eisen’s book….I started looking at some of the top meetings in my own field to gauge the representation of women on the invited speaker list…. Let’s start with some of the premier meetings in our field…. those where the biggest of the big present, attend and send their trainees…

I give you the invited speaker list for the 2013 Cold Spring Harbor Microbial Pathogenesis and Host Response Meeting… girls in red

Keynote Speaker
Jeffrey Gordon, Washington University

Invited Speakers
Theresa Koehler, University of Texas, Houston
Brendan Cormack, Johns Hopkins University
Raphael Valdivia, Duke University
Christopher Sassetti, University of Massachusetts
Russell Vance, University of California, Berkeley
Juliane Bubeck Wardenburg, University of Chicago
John Rawls, Duke University
Anthony Richardson, University of North Carolina, Chapel Hill
Craig Roy, Yale University

Don Sheppard, McGill University, Canada
Suzanne Noble, University of California, San Francisco
Gerry Wright, McMaster University, Canada
Jeffery Cox, University of California, San Francisco
Terry Roemer, Merck Frosst Center for Therapeutic Research, Canada
Lori BurrowsMcMaster University, Canada
Pradeep Singh, University of Washington

That’s 4 girls (that I can tell), out of 17 total.

C’mon – we can surely do better than this.


What is #reviewdouchery?  The short answer is that reviewdouchery are the comments and habits of reviewers that we love to hate. A few random examples (not in order of douchiness):

1. “It would be ‘nice’ if the authors would do these 25 (very expensive and unnecessary to the thesis) experiments.”

I mean, WTF people. I don’t give a rats’ ass about what a reviewer thinks would be “nice”- what I do care about is whether or not a given experiment is essential to proving or disproving the hypothesis that is addressed.

2. 3 page and 30 point reviews accompanying a decision to reject.

Double WTF. If you think a paper should be rejected- a skillful reviewer shouldn’t need 3 pages and 30 detailed points to justify that decision. You should be able to find the fatal flaw and lay that out in a brief single paragraph. Sometimes I think that we have evolved reviewing into proving to the author, the other reviewers, the editors and ourselves that we really ARE smart. And well, that’s just messed up, as my 15 year old would say.

3. Asking for the next obvious experiment.. that might make FIGURE 14.

Data inflation people, I mean do we really think the authors who are living and breathing that work didn’t think of that?? How much data do we REALLY need in a single paper? Do I need to say more. Not a substantive comment.

4. Why don’t you JUST repeat this experiment in elephants!

I mean- the use of the word “just” coupled with what is REALLY REALLY difficult to do- is well, ‘just’ kind of frustrating.

5. Picky comments about terminology that are actually incorrect.

K. If you are going to be type A about terminology- at least get it right. No one likes a know-it-all, and know-it-alls that reek of authority but don’t know shit from shinola… just kind of bothersome… albeit easy to rebut.

I’m sure I’ve done many of these myself… please add your particular favorite bit of #reviewdouchery in the comments…

Adding to the Indirect Cost Chatter

Mike the Mad has a post up this morning in response to a post by Proflikesubstance regarding overhead... aka ‘indirect costs’. In this time of shrinking budgets I think that this is an important conversation to be having… but something caught my eye in PLS posts that I think is worth mentioning.

First, what are ‘direct’ and ‘indirect’ costs and what are they to be used for? From the NIH Grants policy statement (Part II: Terms and Conditions of NIH Grant Awards) we find this:

On direct costs:  A direct cost is any cost that can be specifically identified with a particular project, program, or activity or that can be directly assigned to such activities relatively easily and with a high degree of accuracy. Direct costs include, but are not limited to, salaries, travel, equipment, and supplies directly benefiting the grant-supported project or activity.

On indirect costs:  See facilities and administrative costs definition.

On facilities and administrative costs: Costs that are incurred by a grantee for common or joint objectives and that, therefore, cannot be identified specifically with a particular project or program. These costs also are known as indirect costs.

So, Proflikesubstance starts out like this….

Among many things, overhead has two major functions: 1) pay for the research enterprise, 2) fund start-up packages. Point 2 is pretty straight forward – a research career isn’t going to get off the ground without funds to create data prior to the first grants rolling in. The first point, however, is where many people seem to have a blind spot. (bold is mine)

Say WHAT? I hate to be disagreeable, but I feel like PLS has it kinda upside down. Based on NIH’s own definitions, its just obvious to me that $$ earmarked for facilities and administrative costs,  running the building (paying for the building, paying janitors, keeping the lights on etc) and the administrative infrastructure necessary to carry out research (compliance, HR, grants administration and whatever else you can think of), should be used for that purpose. And although I’ll grouse privately and maybe not-so-privately about the huge hulking disparity in the IDC return for different institutions (some institutions get near 100%, while others get only 50%)- I recognize that some institutions have a budget from the taxpayers of their fair state to defray some of the cost of keeping the lights on, while private institutes generally do not (we can start a whole different argument here).

But holy cow- I don’t get that #2 is “pretty straight forward”. I’m not sure that that is even allowable by NIH rules to use NIH IDCs for start-up packages for new faculty.  I agree that it is probably happening in many institutions- via some indirect route that is not totally transparent. YIkes!