Archive for: December, 2017

More thoughts on getting funded - Nature article

Dec 29 2017 Published by under Uncategorized

Ok, Ok, I am letting go of what pissed me off from this article.

Here is another thing about which I have written before.

Talk to the Program Officer: Programme officers, also called programme directors, are NIH employees who shepherd grant applications through the system, from submission to award. Their role includes advising investigators by e-mail and on the phone — but not every scientist takes full advantage of this opportunity.

When I wrote about this in the past, or when DM wrote about this or datahound wrote about this (here and here and here and lots of other places, too), we got comments back that said: well, yes, but they never answered my phone call or email.

So firstly, the ways to do this. No one likes cold calls, ie, out of the blue from people they don't know. PO's are no exception. They usually have an admin person screening for them. A better strategy (and I have asked PO's about this) is to send an email. Yes, you are the generation that doesn't do email. But the PO is. Send a polite email. Use an appropriate subject line that includes the 5 word version of your proposal. "Discuss potential proposal on Bunny Hopping". Keep the email short:

I would like to discuss a proposal I am developing on Bunny Hopping. [insert one sentence summary of the proposal here]. I believe that it might fall within your portfolio. Is there a good time when we could discuss this on the phone?

If you have an abstract or SA developed, or even a para summary, you can attach it or paste it below. But if you make the PO wade through the whole summary before getting to "can we talk?", they may never make it there.

This of course assumes that you have bothered to read what is in the PO's portfolio. You can find this on the web. The NIH website has lots. Go to the IC you think is relevant. Go to the "extramural page". or just search on "program officers". It is absolutely fine to contact multiple PO's. They will not perceive you as cheating on them.

Now, if that doesn't get a response, try again in a couple of days to a week. Remember these guys are human beings. They have families and get to take vacations, and may even have more work than you do. Sometimes it takes a while.

If after multiple tries, they don't get back. Try another PO. Try the head of the PO's. They may have 40 of these emails, and it could be that yours is the least interesting to them. PO's also run the range of human beings: some are helpful, some take an interest and some are jerks. I've met all kinds in my life.

Finally, don't ever text a PO. Mostly their contacts are land lines, so it most likely won't work. But, texting is how their kids talk to them, not their PI's.

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Getting Funded -thoughts on the Nature Article

Dec 28 2017 Published by under Uncategorized

There is a new piece up in Nature's N&V about getting funded. I'm irritated by the figure, which breaks the old/young distribution in a way that makes their point, but is not defensible on data analysis grounds (let's not even talk about breaking continuous distributions into discreet categories).

But there are some nice little gems tucked into the article.

Taking a modular budget, especially in light of the yearly budget-slimming cuts that the NIH applies to all awards, might hurt a young lab’s research. And the data suggest that it won’t improve the chances of winning a grant.

One of the things to keep in mind is that the budget, modular or not, is a minor, very minor part of the review, and technically not something that gets included in the scoring.

Separate out the scope of the work from the budget requested to do the work. Scope is a legitimate criterion: can the PI do the work proposed? Is it reasonable for the time requested? One of the big flaws I see is that a young PI is proposing to do a 30 year study, and not a 5 year one. But the money? Unless you are asking for Millions a year and a 20M$ overall budget, don't sweat this. Ask for what you need to do the research.

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quote of the day: Almost New Year Edition

Dec 27 2017 Published by under Uncategorized

The past is finished. There is nothing to be gained by going over it. Whatever it gave us in the experiences it brought us was something we had to know.  ― Rebecca Beard


Those who cannot remember the past are condemned to repeat it -George Santayana 

Less nonsensical, but still.

Things are not black and white or green and blue. Forgetting the past and not knowing history opens one up to manipulation by others (and lots of current examples of that - starting with "bringing Christmas back to us"). But dwelling in the past is to deny the life we live now.

Happy New Year to One and All


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Integration of the Curve of Little Deeds

Dec 27 2017 Published by under Uncategorized

There's a meme going round twitter, to list the three things (most important) that you accomplished.


Doc Becca owned it:

I have tried several times to answer this. The trouble is my distribution of accomplishments is very flat, or rather, like the distribution of outcomes when you roll a die: everything is 1/6. I think of these three, and then of  those three, and then these other three.

Which leads me to this thought:

I didn't have a major event like Dr. Becca. I had lots and lots of little and small things, none of which stick out as One of The Most Important Personal Accomplishments.

So what are my small deeds? I gave away more than 10% of my income (if you need a nudge: Donor's Choose). I listened, without judging, to all sorts of people: my trainees, the folks who work in my lab, my friends, my step-ish kids, my family. I dealt with problems large and small in my lab, and made sure that even when things were rough, people felt that they were heard and problems were equitably solved. I was kind to people who were not kind to me. I did some good science, and got some good things published. I made life better for others, without their knowing it was me doing it. I stepped up when someone needed to, but did not fail to take care of myself. I loved, and got love back. None of it spectacular, or reaching the level of yes, these three points on the distribution stand out. In short, I lived.


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NIH changes submissions, again

Dec 21 2017 Published by under Uncategorized

I received the following today (and they didn't even call me "dear"). Before you do anything, talk to your grants office. Remember, you do not submit proposals, your University does. You are not awarded the grant. Your University is. Do not go down a pathway that you discover, on Feb 1 for Feb 5 submission is not what your University permits.

NIH grant applicants: downloadable forms submission option retiring Dec. 31

 NIH Grant Applicant,

 On December 31, 2017 will no longer allow grant applicants to download an entire application form package as a single PDF for offline data entry and later submission.

 Since you were involved in a grant application submitted using downloadable forms in 2017, we wanted to provide a final reminder to switch to one of the following submission options for 2018 submissions:

 1.     NIH’s ASSIST (learn more)

2.     Institutional system-to-system solution (if your institution has one)

3. Workspace (learn more)

Our submission options page can help you compare features and considerations for each option. Ultimately your office of sponsored research or other group responsible for grant application submissions will decide which option is the best fit for you and your organization.

 If there is no business reason to choose one option over another, give NIH’s ASSIST a try. It’s a user-friendly, online solution optimized for NIH applications.

 Although will stop presenting their legacy downloadable forms package as an option at the end of this year, and NIH systems will continue to process previously downloaded application packages through March 2018.  If you plan to submit a downloadeded application package after December 31, 2017, you might want to consider downloading an extra copy of the forms package for the opportunity before Dec 31 just in case you run into a technical difficulty with the original.


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Vice Admiral Amilyn Holdo

Dec 21 2017 Published by under Uncategorized

Holdo Rules. This post gets it, close to exactly. So, no spoilers (here, but yes at the link), but she's great and has purple hair.

I did not go home and clean house last night. I did not do laundry or work on that manuscript or read the postdoc's revisions to the neverending paper. I went to see The Last Jedi. 


A movie with grownups. A movie with older people being heroes and not just slipping into the haze of dementia. A movie that is not just about young people doing things, allegedly in real life, that are well beyond rationality.

(Small claim to fame: I saw the first one, which in the day was just called "Star Wars", in the theater, the day it opened. The theater was half empty and only filled with the college sci-fi nerds like me. It didn't catch on for a week or so. Also saw ESB and RoJ on opening days. That was much harder).

I want to be Holdo when I grow up.




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12 Months of Mistress of the Animals

Dec 21 2017 Published by under Uncategorized

Okay, this is a thing. I've not done this before, but since IBAM is doing it, so shall I. It's the 12 month review of blog posts. It's the first line and a link to the whole post of the first thing from each month.

December: No smoking almost everywhere.

November: Medical School funding is one part of the problem that is driving the issues with career pathways, also known as the too many mouths at the trough problem.

October: I went to NYU to give a talk.

September: One of the hardest things to learn is how one’s effort translates into output.

August: I have frequently written about problems with trainees and what to do about Problem Trainees.

July: I am sorry, but I am actually doing science!

June: Sometimes the current incarnations of culture wars  spills over into the NIH grantsmanship (grantspersonship?) arena.

May: Power often corrupts and absolute power often corrupts absolutely, but the greatest corruption of all comes from withholding power, which grants victory to tyrants. -- Shlomo Riskin

April: When I was at MRU, I lived near the hospital and walked to work.

March: First, a word about exhaustion.

February: Wally wrote: (edited a bit for space, but go read the whole thing) I love being a postdoc – ... we don’t always have choices as to where we live.... Further, some of us belong to minority groups and living in some places in the US (where costs are often far cheaper) is just not particularly safe.

January: This post is my attempt to reduce my grumpiness index.


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The balance between contentment and challenge

Dec 20 2017 Published by under Uncategorized

Balance or tension. On one side is understanding where one is and what one can do. There are extremes: I cannot fly but I can walk across the street. On the other side is the challenge to do more and not accept those limits: I will make that audacious pitch to the potential donor and explain why this work is worthy.

I may want to be tall and strong and have different features. And maybe in some science fiction future that will be possible. But right now, I'm old and short and have nose my genetics gave me. I can want to change those things, and with surgery and lifting weights and enough money, I could change them, some. But I won't ever have the physique of Venus or Serena. And I won't be 30 years younger. To be content with the way I look means more energy for other things, means a happiness with life that I value. But looks is not where the tension has meaning in one's life. It's about what one choses to do.

The other side is, in our culture, the myth of the striver, the outsider, the challenger. The person who doesn't accept and goes on to Change Things in A Big Way. This goes back to the LeGuin story of Omelas, that I touched on here. If you've not read it, do. It's challenging. Sometimes the Changer isn't big and strong and noble, just someone who knows right from wrong. We all take a little of that person with us when we do science. It's part and parcel of the process. We don't do the science that was done 10 years ago. We have new things we want to find and discover. [Although see this on the myth of science as "the miracle machine". ]

So limitations or exploding them. Sometimes those limitations get in the way of doing what we want or even what we know we can do. Imposter syndrome travels this subway line. What is a real limitation, and what is the cultural readout we've internalized? What is wanting to fly?

I think about these tensions. I'd like to say "everyday" but most of the time I am probably just moving forward with the tasks at hand. But, everyday, or maybe not quite everyday, I think about these tensions. There is a progression with age, but still, I want to Do The Big Thing in my science. And I am acutely aware of my limitations, my trainees' limitations. I don't want them to get lost trying to fly. But I don't want them to be stuck thinking that they can't, when they can, and so much more.


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A teacher's reaction to forbidden words

Dec 18 2017 Published by under Uncategorized

The CDC has just released a list of forbidden words:

Policy analysts at the Centers for Disease Control and Prevention in Atlanta were told of the list of forbidden words at a meeting Thursday with senior CDC officials who oversee the budget, according to an analyst who took part in the 90-minute briefing. The forbidden words are “vulnerable,” “entitlement,” “diversity,” “transgender,” “fetus,” “evidence-based” and “science-based.”


Other CDC officials confirmed the existence of a list of forbidden words.It’s likely that other parts of HHS are operating under the same guidelines regarding the use of these words, the analyst said.

The only reason we know this, now, is because someone leaked it. The implications are for policy decisions and budget requests for the coming year. This all feels very Orwellian (time to reread 1984 and better yet Farenheit 451).

It is not at all clear why the words are being forbidden, at the operational level (as opposed to the higher levels desires of the people in charge). I read somewhere that it was a recommendation for getting approval from either Congress/Executive Branch, which sees these as trigger words. However, it is clear that whether it is externally generated censorship, or the internal kind that comes when the author is too aware of what others don't like and self-limits, it is not going to be a good thing for science.

But censorship is censorship. And I teach at a public medical school in a purple-ish state that has had its political tilts to the left and to the right.

I use one of these words in teaching: fetus.

Fetus has a specific meaning for clinicians and developmental biologists. For OB-Gyns, and neonatologists and pediatricians. For people who work on developmental biology in mammals. For people who are trying to make life better and understand the grandeur of life.

I have taught embryology for over 25 years to various and sundry populations of students. We use the word "embryo" for the period of time called "embryogenesis" which lasts roughly from fertilization through 8-12 weeks. During this time organogenesis happens: the formation of organs from the original single fertilized cell. The next period is the "fetal period" where largely growth and maturation occurs (as opposed to new organs forming). "Neonatal" and "Perinatal" are the time around birth. There are some finer points here, and different people studying different aspects have slightly different definitions.

But, to all of us the word "fetal" means something very specific about the biology and physiology and anatomy and development of what is occurring. We use words, we define words, so that we can have a conversation about things without having to resort to extra pictures of waving our hands. Commonly defined words serves the important purpose of mistakes from happening.

As an exercise, go do the "1000 words" thing. Try to describe something using only those words. Its a fun game and ..... But it is difficult for scientists and clinicians to do this as more than a game. We use specific words. We need specific words.

And I use many of those specific words every time I teach. Not just embryo, but uterus and placenta and synsciotroph (tissue that makes the placenta possible).

If you start telling me what words I can use to teach. If you start telling everyone who teaches the next generation of clinicians, not just physicians, but nurses and physical therapists and respiratory therapists and everyone who needs an understanding of anatomy and physiology and neuroscience to take care of infants, what words they can use, we will have a generation of people who cannot do their job  as well as is possible.

One of my favorite lectures to give, and judging from feedback, one of the lectures first year med students like the best is "The Fetus as Patient". There are so many things I could talk about, but I focus on a few, to do them better than running through a shopping list of what can go wrong. I cover what are identical twins, how is a placenta formed, and importantly what is the circulatory system before and after birth. These are all sources of "birth anomalies" things that are clinical problems for infant and mother. But if I can't use the word fetus (and what comes next? pre-natal? placenta? umblical cord?), it becomes harder to give this lecture. It becomes harder to teach. It compromises what these students know and how they will take care of their patients.

Forbidding the use of words is something that never ends well. It does not make the words go away. It limits how people can communicate, and in the case of medical words, it will surely compromise the health of someone.

See also: Mike the Mad Biologist on this.


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Powerful Answers to Imposter Syndrome

Dec 15 2017 Published by under Uncategorized

One of the most powerful antidotes to Imposter Syndrome is actually doing something well. Or, better yet having someone else acknowledge that you have done something well.

We are all hugely sensitive (well, maybe not quite all of us) to the false "yes, lovely" that comes from people who haven't read the manuscript or were texting on their phone throughout one's entire presentation. You know: the review that is one paragraph that says "this is a great paper, and they just need to change this one line in the methods". And its obvious the reviewer just went looking for something to object to, so it didn't look like they hadn't read the paper, which of course, they hadn't. Or that person who you know wasn't paying attention and then says at the end "great talk" (we would all like to be John Tukey, who famously did crossword puzzles through seminars but always had a great question to ask at the end. Yes, Tukey comparisons Tukey. But we're not. Put that damn phone down.).

Recently, I had a paper come back from review. It is a good paper. I knew it was. But I would still go to bed at night thinking: it's horrible. it's irrelevant. no one will appreciate it. Although, to be fair, this latter is frequently true despite quality of content.

The two reviews of this manuscript each vied to be Reviewer Three. Each review was about 2 single-spaced pages long full of, by turns, insightful and irritating comments about what was wrong and needed to be fixed. What mattered was not that one of them didn't get it and that the other was very very picky. I will slog through making the changes. What mattered were a couple of things embedded in the reviews. Rev 1:

The premise of this study is of great interest. The contribution of the sensory and motor aspects of the hopping nerve to locomotion execution is an important question and would make an important contribution to the literature. 

And later on in this review:

I believe the authors are capable of filling in the necessary details to help readers place the significance of these findings into the larger picture of swallowing sensorimotor controls.

Of course there is the start to the second review:

Overall this was a weak manuscript for several reasons. 

Kill me now and put me out of my misery. But here is how Rev 2 ended the review:

Overall if a major revision of this manuscript were done as suggested, the results could have importance to the field. Certainly, the bunny hopping model is original and these data are only available from this laboratory.

A few small bits embedded in each review that spent pages detailing the failures of the study. Yet they made a difference. Two people, who judging by their concerns are working on human hopping and coming at the question from very different ways that my lab does, thought there was something redemptive in this paper. So did the AE who didn't just reject it. I've had better and more positive reviews where the editor says: don't bother resubmitting, and by the way you are a useless piece of draff (points if you get the scifi reference).

It's my task for the next two weeks to try and make some of the changes (moar tables! more figures! more discussion!) and answer the rest. I can only read they critiques for so long before I either get depressed or angry or hungry. It's a small thing to give honest praise, but it's the small things that keep us going.



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