Archive for: November, 2017

quote of the day: jazz musician edition

Nov 16 2017 Published by under Uncategorized

The memory of things gone is important to a jazz musician. Things like old folks singing in the moonlight in the back yard on a hot night or something said long ago. ― Louis Armstrong

Not just musicians.


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One more down side of caring for elderly parents

Nov 16 2017 Published by under Uncategorized

There has been a lot of press about childcare at SfN. InBabyAttachMode reposted her excellent post from a while back. This included this link to a document titled Recs for making SfN 2018 more family/breastfeeding-friendly from Rebecca M. Calisi Rodriguez @BeccaCalisi.  The document makes for interesting reading. I can't believe for example, there are no sinks for handwashing in the lactation rooms. [aside: follow @BeccaCalisi, she's good].

We have come a long way in the six years since IBAM went to SfN and even more in the 30 years since my generation was parenting young ones, and left children at home, as there was no such thing as child care, etc at meetings. I perceive this as changes for the good in our society (when sometimes it feels like there aren't any, also no smoking. In the olden days, the poster areas had a heavy bluish cloud of smoke hanging everywhere).

What I do want to point out is that there is no movement, no support and really no on-site alternatives for people who are care-givers for their elderly and demented parents. People still coo over infants (well, many do). And those who are not enamored of other people's children, at least find it tolerable. I suspect if one went through the posters with one's drooling and unkempt parent, it would not be received so favorably. We tolerate drool and pee and bodily smells in kids in ways we do not in adults. Using a "family restroom" in public to change elder diapers is seldom met with tolerance and approval.

I'm not necessarily arguing that what we provide for childcare should also be mirrored in adult-care. But we do need to be aware that all of the social burdens of taking care of others are not just breastfeeding infants.

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George Will gets it

Nov 15 2017 Published by under Uncategorized

I'm not a terribly big fan of the op-ed political columnist George Will.

But he's got an op-ed in the Washington Post that makes some good points about academia and the Republican Rush to tax endowments.

Yes, its only the "very rich" universities. And why shouldn't they (as in the very rich corporations and the very rich individuals) pay their "fair share"?

Because [some subset of us] believe that Universities are different from other large corporations. [set aside the concerns that Universities have a product. Set aside concerns that Universities are being run like a corporation. these are important discussions. just not here, not now.]

So before I start on what was good in Will's piece, the idea of universities being different does bring me to one of my problems with Will's piece: its reeks of the exceptional attitudes that the owning class uses to justify it's own existence. The piece uses Princeton as an example, partly because, as Will discloses, he was once a trustee of Princeton. He says:

Great universities are great because philanthropic generations have borne the cost of sustaining private institutions that seed the nation with excellence.

Yes, but also, depending on how far back in history you wish to go, there are some problems with this. Firstly, this excellence was carried out on the back of enslaved peoples. This must be acknowledged. And dealt with. Secondly the definition of "excellence" has evolved with time, and certainly excluded not only people of color (once free), but also Jews, Asians, and in general anyone who wasn't deemed as having the potential for greatness. Even now, there are arguments about the percentage of Jews and Asian-Americans who belong at such great places.

Will has clearly been sensitized. He points out what Princeton has been doing to rectify this, and that legacies (children of alums) are only 13% of this year's entering freshman. And that this endowment drives financial assistance for the those that are not part of the financial elite. I think the Major Private Universities still have a ways to go in addressing these issues, but its a lot better than when I was going to college, and that was better than when my parents went.

Moving past these issues, albeit for a moment, there is value in things that Will says in this piece.  He explains, with some clarity what  "supervisory taxes" are, taxes that are imposed on private foundations, as well as what a "operating foundation" is (link from his article). These are important legal distinctions that impact on who pays taxes and how much. We can turn up our noses at boring legalese, but if you want to fight the battles, you need to know what the ground rules are. This falls into the same basket as getting Al Capone on tax evasion.

But the thing that I found most interesting in the article, especially in the light of the current tax bills working their way through Congress is Will's continuing commitment to small government. I may not believe in small government, nor in the standard libertarian line, but part of what frosts my shorts about the current legislation is that the current hypocrites-in-charge are fine with "reduce government" except when it comes to things that their corporate puppet-masters deem important. Thus, we have a run-away bloated military. Republicans are all about "limiting the budget deficit", except when they are not, for political reasons. Here is the damning paragraph from his piece:

Government having long ago slipped the leash of restraint, the public sector’s sprawl threatens to enfeeble the private institutions of civil society that mediate between the individual and the state and that leaven society with energy and creativity that government cannot supply. Time was, conservatism’s central argument for limiting government was to defend these institutions from being starved of resources and functions by government. Abandonment of this argument is apparent in the vandalism that Republicans are mounting against universities’ endowments.

I am outraged at what the Republicans want to tax and what they want not to tax. The hypocrisy, it burns.

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Interpreting Pink Sheets part 2

Nov 14 2017 Published by under Uncategorized

Category: Critiques of Premise. Premise can be hard to interpret what is wanted and what is meant. But basically, you answering the question of "what has been done to suggest that this project is interesting/going to change things?".

This is from Rev 1:

  • While the proposed studies are potentially significant as they may have great translational implication, the proposal suffers primarily
    from the lack of strong scientific premise. 

Here is an example of premise critique (from these reviews, but with subject matter obscured) that is hard to understand. Background: there exists a human pathophysiology (say ConditionA). There is an intervention (InterventionB)that causes some problems (ProbC) . The proposal is to use an animal that mimics CondA, determine the mechanism that makes for the problems associated with IntervB, and proposes a potential way to address those.

It is questionable that the proposed animal model mimics the physiologic problem in [the group of patients proposed here] who have had the standard clinical intervention. The applicant did not make it clear that if the pathophysiology observed in this model [to mimic  the human initial problem, not the intervention] is attributable to the problem human patients, or a simple consequence of making the model. This model was initially developed to test [something else from the PI]. Thus, the previous publications and preliminary results do not support the scientific premise.

How to parse this? My reading: the PI had an model that was good for looking at some other aspect of physiology, but decided that it actually mimics CondA, the human problem. The reviewer points out that the model proposed for CondA has not been validated for CondA. And therefore because the project involved creating CondA and then applying IntervB, the project couldn't tell if the result, ProbC stemmed from CondA or IntervB.

The PI and team could show that their model of generating CondA followed by IntervB duplicates ProbC. The trouble is, are they really testing IntervB?

Rev 2 echoes these concerns:

Scientific Premise: The investigators provide no background or supporting preliminary data in the Significance section. The background provided in subsequent sections is very superficial and does not adequately support their proposed project.

Remember, this proposal did not get discussed. Therefore, Rev 1 & Rev 2 had the same thoughts independently. When our proposals get triaged & not discussed (yes, our, I've been triaged many times) it hurts. Yet, when the reviewers have the same concerns, this is a big red flag being waved.

Especially because here is Rev 3 on premise:

There is no specific statement of scientific premise. The central hypothesis is that [IntervB] causes [ResultC] through three nonexclusive mechanisms... Each of these could contribute to [CondA].

This is exactly the same problem as Rev 1 & Rev2. However, this isn't obvious immediately if you just read through the reviews. The strategy I find useful is to go through a collate the problems across reviewers. Find what each reviewer says about premise, about significance, about innovation. Line up the comments by topic. Then things like this jump out at you.

Writing this and the previous post took some effort on my part. The reason for pointing this out is to say that reading and understanding reviews takes some effort, even when its your proposal, your own best beloved baby. And one must be prepared to perform radical surgery on that best beloved. Here, rewriting to address this problem is not going to be easy. The group needs to consider the model they are proposing and why it works the way it does. But if they just brush off this criticism with a one sentence reply, or include a statement in the significance that says "The premise of this work is.." and re-iterate what they have said before, they will not get funded. Even if they had entirely different reviewers. These reviewers are all saying the same thing and all seeing the same problem. Take this as the gift it is, address the problem, and work towards funding.

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Quote of the day: cold hard realism edition

Nov 13 2017 Published by under Uncategorized

Your whole life people tell you to do what you love. But if you gotta do something else to pay the bills, you don't automatically have to be miserable. --Jeph Jacques


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Looking at Pink Sheets / NIH reviews (part 1)

Nov 13 2017 Published by under Uncategorized

A former trainee, now working with in a medical center/research group/structured environment, asked me to take a look at the reviews for their recently triaged proposal. While I have permission to quote these, I've done everything I can to cover up identities.

There are a number of interesting points worth learning from. In particular, a number of things that were constant across reviews. I have put the reviewer comments in italic to differentiate from my thoughts.  I will  try and organize these into categories.

This is where this post got long, so just one category today:

Category: Obvious things that you should pay attention to ... or ... the reviewers are saying exactly what they mean. This is reviewer 1:

  • Major weaknesses are the dependence of Aim 3 on success in Aims 1 and 2: This is obvious. If you need the results from aim 1 to know what you will do in aim 2, what happens if aim 1 fails? This is a difficult thing, as one is usually trying to build a series of steps. And frequently, what we find in the beginning changes what we find later on. But Aims need to be independent. One way to cope with this is to rearrange what is in each aim so that something you might vary within an aim, becomes the difference between the aims.
  • [major weakness includes]: a lack of scientific rigor. Guys, NIH is serious about this premise and rigor stuff. We were told before and at study section to explicitly mention these words in our reviews. See here. and here. Many of the specific comments in this review are about rigor.
  • Although the clinical need is clear ... the weaknesses outweigh the strengths of the proposal. Ouch. Being clinically relevant is not enough. Being translational is not enough. The proposal must stand on its research merits.
  • For Personnel, I've seen (and written) versions of the following comments over and over. These are all about picking a project that is feasible. Feasible is not an explicit criterion, but it comes up in study section discussion all the time:
    • This team does not have a long history of collaboration
    • The ability of the PI to direct such a large project is not proven.
    • The proposal would be improved by an explicit plan for regular communication and coordination of the efforts in the diverse labs involved.

Here is a list of simple things that should be in every proposal. These are all about rigor of the proposed project. This is reviewer 2:

  • What are controls?
  • Expected results and interpretation are not provided in each aim.
  • Sample sizes are very small. And  the numbers in the human subjects table do not match either those in the research design for Aim 1 or Aim 2. 
  • Sex as a biological variable is not considered.

Which brings us to this reviewer's conclusion for Approach Weaknesses:

  • Thus, scientific rigor and reproducibility are a concern.

Reviewer three continues with this theme. When all three reviewers hit the same point, in this case lack of rigor, one must stop and reconsider the proposal.

The proposal suffers from numerous problems ranging from a lack of clarity, superficial background, and contradictory statements. Details of the actual research are lacking as is identification of who will actually carry out the research

At the end of one of the reviews are the following famous words. Some people see this as a Stock Critique. It can be. But in this case it was the reviewer summarizing why this proposal got "7's" in Approach.

The weaknesses reduce the likelihood that the project will have a sustained, powerful influence in the field.

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Science Nerd Humor

Nov 12 2017 Published by under Uncategorized

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How to do a (paper) review right

Nov 10 2017 Published by under Uncategorized

Ok, first from the editor:

Please note that both reviewers are demanding MAJOR and extensive revisions, so please keep this in mind if you decide to revise and resubmit the paper, as the revised version will be reevaluated by the original reviewers. Please be aware that this invitation does not guarantee eventual acceptance of your manuscript.

Translation: be afraid. be very afraid.

Then, the editor gives a page of logistics/style points/file considerations and demands. blah blah blah.

Let's get to the the reviews. No reviewer three, so reviewer two steps up to the plate:

Reviewer two:

Overall this was a weak manuscript for several reasons. 

Translation: just go die in a corner.

Followed by a page and half of detailed, single spaced criticism of everything.

Translation: don't give up your day job.

Potty: but this *is* my day job.

Reviewer: Find another.

Now on to Reviewer One:

The premise of this study is of great interest. The contribution of the blah blah aspects of the leg nerves to bunny hopping execution is an important question and would make an important contribution to the literature.

Translation: there is hope for you, yet, kiddo. But don't get cocky. Then follows a page and a half of detailed, single spaced criticism as to what is wrong. In detail. Excruciating detail.  Translation: do not fuck with me, monkey boy.


But why did I title this post "doing it right"? At the end of Rev 1's review was this line, that I missed the first time through (take home message: read the fine print):

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 bunny hopping.

Thank you, Reviewer One. Thank you.

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Quote of the Day

Nov 09 2017 Published by under Uncategorized

I discovered that rejections are not altogether a bad thing. They teach a writer to rely on his own judgment and to say in his heart of hearts, 'To hell with you.' -- Saul Bellow

This applies to writing papers, and probably grant proposals, too.

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Get ready for winter: Pandas playing in the snow

Nov 09 2017 Published by under Uncategorized

I too want to roll down the hill.

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