Archive for: May, 2014

Reading Between the Lines about Scientists

May 19 2014 Published by under Uncategorized

There is a superb New Yorker article about a method to retrieve lost fragile early recordings of music. This music was recorded on wax or piano rolls. Playing them now is likely to destroy them, or alter the sound. The article is unfortunately behind a paywall (so no link).  But here is something from the Library of Congress about the workHere is something from LBL. But what I have to say is tangentially about the story, and more about the hero, a physicist named Carl Haber who works at Lawrence Berkeley Labs. Haber heard Micky Hart (for you millennials, he was the drummer for the Grateful Dead, and let's not get started talking about the Dead. not now) talking about the archives of aboriginal music and how they are being lost. These archives were collected by people around 1890-1940, and the collectors only cared about the words, not necessarily preserving the music. It wasn't a thing back then.

Anyway, Haber is an applied physicist who builds stuff. He worked on a way to align the detectors at CERN without touching them, and realized that it would apply to lots of other stuff. He heard Micky Hart and as they say in the science biz, a light bulb went on. an alarm went off. Sometimes things go on for significance, and sometimes they go off. I digress.

This was the first thing that got my attention. Experimental scientists are often/always/most of time looking at the rest of the world as interesting problems, or interesting questions, or very interesting what-ifs. But they/we/you are looking through the lens of what we know about problem solving (this is not a bad thing). Lots of my best ideas about my work have come from talking to someone else. And usually not someone who cares about bunny hopping as much as I do. Sometimes its about science, and sometimes its about something else entirely. And then.. mental thwap... a connection is made. Some people say being open and curious is not something you can learn. I disagree.

There are two parts of being open to new ideas. The first is learning to listen. Not just waiting for your turn to talk, but listening to and hearing what someone else is saying. And not just when they are talking about something you already care about. Yup, there are boring people out there, and you can make a type I error, thinking someone is interesting when they are not. But there are lots more type II errors, of missing interesting people.

The second part is having enough security in who you are to be able to listen, to be able to not talk about yourself, and to appreciate excellence in others. It's easier when you've just had a paper published, or been invited to submit a full NSF proposal. And there is no shame in taking time to lick your wounds after a stinging rejection. You are the expert in you-ology. You know what you know. You are good at it. You do not have to prove it to everyone. This takes time, and I know lotsa greybeards who have not mastered this (the chair from hell, for example).

Back to Haber. The story talks about how he and a grad student, Vitaliy Fadeyev built a machine to read and play old wax recordings without touching them. It was based on visual imaging. Fadeyev sort of gets lost and neglected by the end of the story. I wanted to know what happened to him.  Here is the arXiv listing for his publications.

The second thing that got my attention was a throw-away line about Haber's history. You know the end part of the beginning of the article where the author goes through how did the interesting subject got to the point of doing the interesting thing that the article is about.

"For more than fifteen years, he was part of a project that discovered the top quark.... When that work ended, Haber was added to the ATLAS team [the international alliance of labs and universities that conduct experiments at CERN]".

OK. When that work ended, he was added to another team. Did he struggle? Was it a done deal? Did he have a say in what happened? Did he have a family, a partner, worries about the future? Did he consider alternative careers? Did he have a mentor who helped get him onto the next project? We all know there is a huge history in that sentence. Many of us have lived that history. It isn't necessarily part of the story being told in the New Yorker. But given the energy that I put into thinking about the people who work with me, the people who get their salaries from my grant, the trainees for whom I am responsible, I always wonder about the gap between the "when that work ended" and "being added to the ATLAS team".






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No-Cost Extensions to Grants (and a bit about carryover funds)

May 16 2014 Published by under Uncategorized

I love the new Scientopia blog DataHound. I was a statistician before I was a biologist, and he brings experience and sensibility to understanding trends in funding. His latest post, on gaps in funding, seems typical of what he is doing. It analyzes the data, shows what happens when a person has a year without funding in terms of getting funded again, and in the end offers insight to the implications. In this case, the world can be an unsure place and that the insecurity  people feel stems from something real in the data.

In the comments about the post, Drug Monkey asks a good question about No-Cost Extensions and how they fit into this analysis. I was talking about this to a colleague and they said "what's a no-cost extension?".  So here's the answer:

The No-Cost Extension feature, accessed via eRA Commons, is an electronic means for a grantee organization to electronically submit a notification that they have exercised their one-time authority to extend without funds the final budget period of a project period of a grant. This extension can be up to 12 months in additional time. This assumes all internal review and approval processes at the grantee organization have already taken place.

In short, both NIH and NSF have a mechanism that lets you extend your grant in time, and spend any money you may not yet have spent. It is mostly automatic. The institution (not PI!) gets to ask for this (one time), and it is fairly automatic. The Signing Officials at the grantee organization (someone in the sponsored research/projects/grants office) are the ones who do the electronic paperwork. This happens no earlier than 90 days before the official end of project. More information for the grantee is here. As NIH says in several places, this is a one-time deal.

There can only be one no cost extension through Commons per grant. If you have applied previously for an extension for this grant, an Extension link will not be available. Any future request needs to be directed to a Grants Management Specialist.

Here is some of the official verbage about NCE's, including the following rules:

  • no term of award specifically prohibits the extension,
  • no additional funds are required to be obligated by the NIH awarding IC, and
  • the project's originally approved scope will not change.

Now  for some implementation and de facto info for PI's. Where does NCE money come from? It comes from something called carryover funds.  In NIH lingo this is:

Carryover is the process by which unobligated funds remaining at the end of a budget period may be carried forward to the next budget period to cover allowable costs in that budget period. The carryover of funds enables grantees to use unexpended prior year grant funds in the current budget period.

Most grants have automatic carryover authority, and grantees do not have to request approval from the NIH in order to carry over funds from one budget period to the next.

In the olden dayes, carryover was money you started squirreling away for a rainy day. Carryover is money you haven't spent. Used to be you could budget wisely and have some left over for the future.  Rules have changed. And have likely changed again. Now, if you carry over more than 20% of your annual budget you need to justify it. Seriously justify it (moving and not doing experiments, have 6 months leave for whatever reason, procreating, honoring your parents, etc). This is from the NIH instructions:

When preparing a justification for a carryover request, grantees should answer the following questions:

  • Why were the funds not spent in the past year?
  • What additional work will be done during the current grant year that is not possible with the budget currently allotted to this year? Thought must be given to how the work will be accelerated; for example, will more staff be hired, effort increased or more assays run?
  • Is the request essential? Are costs reasonable, allowable, necessary and in line with the existing budget? Are there new costs that were previously unforeseen? How will the work be impacted if the funds are not carried over?

I know two people, who in the last year requested carry-over of about 18% and were questioned by NIH for not spending the money. The message at this point in time is very clear: NIH is hurting and money you didn't spend is obviously money you don't need, and NIH might take it back.  NIAID even says:

NIAID funds you by budget period (usually one year) and expects you to use funds during that budget period.

BTW, here is a link to "Pay attention to how you spend your money" from NIH. This is worthy of its own post. Soon to follow. Promise.  But the most important message about this is: Don't depend on your institution to monitor your spending.

Back to carryover. Why do you want it, and why is a NCE a Good Thing. Part of this is about timing for your next grant. Its good to have some carryover so that if you are not immediately re-funded, you are able to do a little bit more if you need that preliminary data. That you are not immediately refunded is becoming more common, more expected and less of a kiss of death. But this money, and a no-cost extension are important, not so much for making your department happy, but to ensure your sanity in the funding process. To ensure that you can keep a lab going. That you can pay the absolutely critical tech. That you do not leave trainees high and dry because you've run out of money.

On the other hand, do NOT stint yourself, and be a cheapskate in getting done what you need to do. I have had junior people ask me about saving each year. The best advice I ever got was: the most important thing you need to do with your grant is get data, analyze it, and publish it. Saving money to carryover or for a NCE is good. But doing the science is better.


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Sex differences in experiments, and the role of animal models experimentation

May 15 2014 Published by under Uncategorized

Drugmonkey has an excellent post about the latest <achtung!> command from LordHighCollins of the The NIH.

I absolutely agree with DM that I would be *thrilled* to do more sex-difference studies/analyses in my work. And publish the results, whether or not they are significant. And explain what my perception of those differences, or lack thereof mean.

As usual, his reasoning hits the nail on the head. It's going to cost a huge amount more. I do animal work with 'real mammals' (ie. USDA species, not rats & mice). In fact they're not rodents. In fact each one costs A Lot Of Money. Animals and their housing are two of the biggest line items on my grant. And, as was mentioned, doubling won't be enough, because it won't permit testing of sex*effect interactions. Given that I'm at the limit for power, I can't reduce sample sizes anywhere else. We do one or two animals at a time. We can't really scale up (they are big animals, ha ha ha, and therefore will hit biomechanical failure with scaling... just a little allometry joke) in terms of person-work-effort, so it will be at least a doubling of time.

I think, however, this kind of misses the argument about the value of animal models. There, I put it in bold italics to catch your attention. Animal models do not prove that whatever we are testing will cure cancer or make disabled children walk again. Animal models give us the basis for what is happening, the mechanisms, the underlying biology.

I receive lots of criticism at the clinical meetings I attend (often from older clinicians who don't understand data analysis and from younger clinicians who are already know everything) for working with animals. Those arguments are roughly: when you do animals you have no compliance issues, you have no problems that these are older/younger/infant people who don't do <whatever> the same way you get your animals to do <whatever>. Animals don't have all the confounding conditions that my patients do. Animals don't have cognition to think about what you're asking them (though I disagree with this, a bit). Animals don't have families who support or don't support the intervention (though they do have my brilliant postdoc and tech).

My answer is to these critiques is "exactly right". With an animal model you can isolate  whatever it is you are testing, examining, discovering from all those other things. If I want to show this whole class of interventions works because of CNS response to peripheral something or other, I am not going to have to worry about all those other factors. I want to know about this set of nerve connections. If it is nerve pathway A, then A1 will help, but if it is pathway B then it won't, but B1 has been shown to do something. In your precious human samples, you have so many factors, that you can't possibly know what is making what else happen.

In fact, I use female animals. They are more tractable. They take less time to train. My supplier will give me a 20% discount if I buy males. I've done that from time to time. They are a pain in the ass. I've seen no real difference in the clinical conditions I'm working with. But my power is low in those tests. The effect size is negligible compared to the condition/intervention effect size. Does that mean its clinically irrelevant? I don't know. Male and female nervous systems are different.  But that is not the main effect I'm testing.  The people who blithely say "oh stop moaning" and "there will be resistance"  "just lie back and thing of Mother England", sex is already their main effect. They frost my shorts.

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Midvale School for the Gifted

May 15 2014 Published by under Uncategorized

I'm still figuring out how Scientopia is working. Note the gerund verb (figuring). Mistakes have been made. Corrections attempted. Eventually I will get a pikkie on the header.

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The College Experience and Culture

May 15 2014 Published by under Uncategorized

I am normally quite irritated by Ross Douthat who can't seem distinguish among being conservative about different things. I for one am more conservative about driving than I am about crossing the street at a busy intersection.

He has had two columns in the NYT about the college experience that young women have. The first one is about the book “Paying for the Party,” which describes the class aspects of current college climate. I've not read the book, and its on my list. Here is the review from Inside Higher Ed. The book talks about how the social life so dominates colleges today, and how people from working class backgrounds are poorly prepared to cope (let alone do not have the money to keep up). The book followed a group of women through their career and documented what happened to them. I do not doubt that this is true. From Douthat:

The losers are students ill equipped for the experiments in youthful dissipation that are now accepted as every well-educated millennial’s natural birthright.

This is where I started to get irritated. This was not my experience when I was teaching college-level biology. This was clearly not the experience of the working class students I've seen in MRU (and other) medical schools, dental schools and other allied health fields. There are people, millenial people, who know what college is about. Who have a clue of what they want and what they need to do to get it.

Douthat has an ax to grind and its that other people are having fun. Not all parties are "libertine". Not all owning-class or petite-bourgeois students are there to spend money and have fun.

But this isn't what I wanted to rant and rave about here. The second column titled "Rape and the College Brand" actually makes a few good points. Always read the people you despise or even the people with whom you disagree. He is still busy trashing what he sees as the college atmosphere or climate "oriented toward heavy drinking and hooking up".

He may be wrong about the reasons for it, but he is right about wanting to talk about:

a more specific and toxic issue in college social life: the prevalence on campuses, often in alcohol-infused situations, of rape and sexual assault, and the question of what college administrations should be obliged to do about it.

There is more stuff I disagree with, but the strong point he makes is how little  campus administration seems to care about this.

The protesting students may be overzealous and unduly ideological, but when you’re running an essentially corrupt institution, sometimes that’s the kind of opposition you deserve.

Corruption is a strong word, but not, I think, unmerited. Over the last few generations, America’s most prominent universities — both public and private — have pursued a strategy of corporate expansion, furious status competition, and moral and pedagogical retreat.

And the point I agree with is (except for the bit about supervision):

But the modern university’s primary loyalty is not really to liberalism or political correctness or any kind of ideological design: It’s to the school’s brand, status and bottom line. And when something goes badly wrong, or predators run loose — as tends to happen in a world where teens and early-twentysomethings are barely supervised and held to no standard higher than consent — the mask of kindness and community slips, and the face revealed beneath is often bloodless, corporate and intent on self-protection.

I was about to disagree with the "held to standards" part, but then I remembered a story I heard last week from a colleague about catching a student cheating, documenting it on video, and then having it dismissed for being "insufficient evidence". This was a medical student.

I understand that colleges, medical schools, universities have to have a budget. They need to pay the bills. But the corporate mentality, including the incredible expansion of administrators over faculty is part of what Douthat is talking about. As long as Boards of Trustees, who are rich business people or political appointees (or both), set the tone, chose the president, and want to run Universities like for-profit companies, rather than not-for-profits that have another goal (education) these problems won't disappear.

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Academic Administration: It's all about money and althletics

May 09 2014 Published by under Uncategorized

One of my loyal readers (and total football fanatic, as I would not have found this on my own) pointed me in the direction of this story about the new President of Youngstown State University, Jim Tressel.

Evidently, Mr. Tressel, currently  Executive Vice President for Student Success at the University of Akron, received an unanimous vote from the Board of  Trustees (which I gather in the State of Ohio is a political plum given to big gubernatorial campaign donors).

His qualifications seemed to be largely running the Ohio State Football program. As  well as:

Tressel returns to the Mahoning Valley [where YSU is] and the institution where he coached football from 1986 to 2000. Since then he coached at Ohio State University and spent two years in administration at UA. [University of Akron].

Here is the relevant information from his wikipedia page:

However, Tressel resigned from OSU as head coach in May 2011 amid an NCAA investigation into rules violations during the prior 2010 season. The investigation resulted in OSU self-vacating victories from the 2010 season (including the 2011 Sugar Bowl).[1]


Tressel's highest level of education is a Master's degree (a Doctorate is virtually a prerequisite for any university president position in the United States), combined with the show-cause penalty that is in effect for Tressel until 2016.

For those of outside the athletic mainstream (again from wikipedia):

In the National Collegiate Athletic Association (NCAA), a show-cause penalty is an administrative punishment ordering (for a limited time) that any NCAA penalties imposed on a coach found to have committed major rules violations, will stay in effect against that coach for the sanction(s)'s full duration -- and could also be transferred to any other NCAA-member school that hires the coach thereafter.

His job at Akron was Vice President of Student Success, a euphemism I am told raising money for athletes. In any case, there is nothing like indicating what title people who have committed ethical violations can get. And important jobs.



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The narrative of your life

May 01 2014 Published by under Uncategorized

At xBio I heard a great talk by Gordon Mitchell, the Comroe lecture. The lecture, about respiratory plasticity and apnea was great. It was not my area, so I was also listening on a more meta-level. What Mitchell did was give the history of his scientific development. Being able to do this is a good skill, and I tweeted so.

Enter, the inestimable Dr. Becca who said "this is how I approached my TT job talks".  So we're writing this together - a double dose of advice. It's good for talks, but it is also incredibly important for any pre-tenure mentoring meetings, and a near necessity for tenure documents.

Doc Becca:

I arranged to practice my TT job talk in front of some folks from my post-doc department, and as was customary for my talks until that day, at the bottom of the title slide I had "Dr Becca, advisor's lab, post-doc Institution." Before I even got a chance to begin speaking, one of the newer TT profs in the audience said, "Take your advisor's name off this slide. This talk is about YOU." This was some of the best advice I ever got in preparation for my interviews. This WAS about me. It's the Me Show! It is not about me representing my mentor anymore. That tiny change helped me frame the whole talk to be about my journey, not just my data. I took my audience through the thought processes that led from my graduate work to my post-doc, and then how I used my post-doc work to carve a niche for myself in my field. And I guess I did a pretty convincing job, because I got offers from both departments that interviewed me. When search committees interview job candidates, they're looking for someone who knows who they are and what they're going to do with their careers- not just someone who's done some stuff in some fancy labs. Your job talk is your narrative, just like your tenure packet statements will be your narrative in another 6 years' time. Do you know what your story is, where it's going?

Back to Potnia:

At my MRU there is a letter that goes in with your CV for your tenure or promotion package. Its called the Dean's letter cause the chair signs it  and addresses it to the Dean (who may or may not ever read it. There is a school wide committee who certainly will). The chair may sign it, but by and large the candidate writes it.

This letter is the narrative of what you have done. It needs to include ideas and data and references to papers you have published. For an assoc prof, its at least 5 single spaced pages, and for full its nearer to 10. Crafting this letter is a skill, and one that you can't start too sooWhat does it look like? It is the story, the narrative. It fills in the gaps in the CV.

To wit:

As a postdoc, I was  in the world's foremost bunny hopping lab. When I moved to MRU, I  started a new program in chinchilla hopping. The first 2 papers I published developed the chinchilla model, and demonstrated the ways  in  which chinchillas were different from bunnies, and the interesting biomechanical and ecological consequences of chinchilla hopping. This led me to do field work on chinchillas in South American and my paper XYZ is an ecological study of chinchilla hopping in their natural setting, something that was unknown until I did this work. While I was there, the chinchillas all  started losing one leg. I first studied one legged hopping in collaboration with Dr. Jose BigWhig, an expert in chinchilla bacterial 8leg disease. Working with Dr. BigWhig, we published papers X3, X4 and X5. I was  responsible for all the biomechanics, but also learned a great deal about bacterial leg disease. When a similar outbreak occurred in North American bunnies, I was able to document that this was the same bug as infected the chinchillas. In fact, it is likely that I was responsible for the transfer of this bug because the outbreak occurred shortly after my return from South America. In my papers Y1 and Y2  I did both the biomechanics and the bacterial disease analyses for the North American bunnies.

This para shows: 1) independnce from postdoc advisor, 2) growth of abilities 3) collaboration and 4) new program.   If this was for real, there would be references to students who worked on the projects, papers presented at meetings, grants etc. Its woven into a timeline of the history and intellectual development.



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