Archive for: March, 2015

Someone doesn't know me all that well: Focus Group Edition

Mar 11 2015 Published by under Uncategorized

In my email came the following. We will ignore bad grammar. We will ignore irritating buzzwords ("stakeholder"). We will chortle at the ignorance of this assignment:

Dear Focus Group: You are invited to this Focus Group on behalf of Strategic Leadership Associates, Inc. and the College of Graduate Studies as an important part of the strategic planning process.  As a key stakeholder, you represent a very important constituent of the College of Graduate Studies and your views regarding its current and future services are very important to the planning process. 

Below, I have listed the logistics of the Focus Group you will be part of:

FOCUS GROUP:                      Graduate Students                                DATE:      Wednesday, March 18, 2015 TIME: 12:45 to 2:15 p.m.  

Your views will be used to help us as we develop a 5-year strategic plan.  Please deliver me ( )an RSVP so that space can be accommodated for.

I have been quite outspoken at my new almost-MRU that we are training too many grad students. That we aren't supporting the ones we have well enough. That saying "well my students get postdocs" is not a sufficient answer. I have been (gently, politely) requested to keep these objections to the appropriate venues and not bring them up at every discussions I think relevant. I am fairly sure that the organizer of this endeavor is unaware of my, shall we say, proclivities?

I do see this as a clarion call for a discussion.

2 responses so far

Another hero dies

Mar 10 2015 Published by under Uncategorized

Another one of my heroes died. Minnie Minoso.


I just found out. So sad. Part of my youth was spent on the south side of Chicago and my father used to take me to White Sox games when I was little. My mother on the other hand, was a die-hard Yankees fan, and was contemptuous of any and every other team. I could say a lot of stuff about race, etc. But he was still Mr. WhiteSox to me.



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Evolution, Perfection and Life

Mar 10 2015 Published by under Uncategorized

Carl Zimmer has an excellent piece in Sunday's NYTimes on Junk DNA, which I have learned is an unacceptable term in some circles, particularly to some of our most favorite NIH directors.

I would say, in terms of junk DNA, we don't use that term any more 'cause I think it was pretty much a case of hubris to imagine that we could dispense with any part of the genome as if we knew enough to say it wasn't functional. There will be parts of the genome that are just, you know, random collections of repeats, like Alu's, but most of the genome that we used to think was there for spacer turns out to be doing stuff and most of that stuff is about regulation and that's where the epigenome gets involved, and is teaching us a lot.- Francis Collins

Zimmer talks to a number of scientists who present some pretty convincing evidence about the lack of correlation between genome size and biological complexity, including the plant with the biggest genome.  The article presents the tension between those, like T. Ryan Gregory from University of Guelph (one of the stars of Zimmer's article) who see lots of junk, and those, such as John Rinn, who are busy looking for things that non-coding DNA do.

As background for the current dispute, Zimmer goes back to Gould and Lewontin and their view of evolutionary mechanisms. Gould in particular, was frequently represented as "not believing in natural selection" because he believed that it wasn't all of evolution. What Gould (read closely) was saying  was that of course, natural selection worked, but it, and evolution didn't make perfection. Exaptation, in his paper with Elizabeth Vrba, succinctly points out that selection often works with what already exists when a new structure evolves. Examples include skull sutures which make significant brain growth possible in mammals exist as joints in ectotherms that have neither large brains nor live birth. The Panglossian concept of perfection, as generated by natural selection, is something that has been argued about for years. The debates about junk DNA are just its current incarnation.

What fascinates me are the folks who object to the concept of junk DNA. Zimmer points out that even if John Rinn finds that "junk genes" have an important purpose, its much more like looking for gold in the sand on the beach. He quotes Alex Palazzo from University of Toronto:  “probably what you found is a little bit of noise.” Zimmer, at the end of the article, comes down firmly on the side of some DNA being junk, and in fact not "a sign of evolution’s failure. It is, instead, evidence of its slow and slovenly triumph". As Zimmer implies, part of this defense of the Human Genome Project, but perhaps there is more going on.

The idea that there is junk, or waste, or nonsense in nature is tough for some people. They may or may not be overtly or classically religious, but slovenly nature, to use Zimmer's word, is an anathema to them. Many people who are in awe of nature, be it towering redwoods, or the intricate dance of genes, find stuff that doesn't serve a purpose, well, unsettling. The explanations of the accumulation of junk DNA, just like the accumulations of non-functional bits of anatomy, just happens. Zimmer, as Steve Gould famously did every year, goes back to Darwin for defense of both other forces of evolution beyond natural selection. What is tough is when the data, be it in the natural world, one's laboratory or genome, don't conform to one's preconceptions of the world.


12 responses so far

Legal Justice League Women of SCOTUS [revised]

Mar 09 2015 Published by under Uncategorized

New Note:

OK, I screwed up. The original post took the post of Maia Weinstock and copied it. I thought I had put in sufficient attribution to make it clear that this was NOT MY STUFF, but an incredibly wonderful post from an incredibly wonderful person.

I was wrong. I apologize to Maia and her readers.

The post below is revised. It includes Maia's images, but none of her text. It is very much worthwhile heading over to her site and reading what she wrote.

I love this.  From Maia Weinstock @20tauri  Go follow her.


I love this because SCOTUS is an incredibly powerful body, with perhaps less accountability than other parts of the government. My godfather argued his own case in front of the court about the First Amendment. I remember when Sandra Day O'Connor was appointed. I remember when she stepped down because of her husband, who had Alzheimer's. The other women on the court have their own powerful stories. And somehow, Lego is a great tribute to these women.

Other things of hers I love:

Grace Hopper:

grace hopper


Temple Grandin:


2 responses so far

All my shorts, today they are frosted

Mar 06 2015 Published by under Uncategorized


That thing that frosted my shorts earlier this week? It's back with a vengeance. Here, with my comments is the latest incarnation:

Dear All - I am not your "dear" anything. Promise.

 This is a slight abuse of the process, No shit Sherlock

but I would like to test your generosity a little further. nope, all of out generosity and out of fucks, too

I am undertaking a XX mile physical feat of unparalleled stupidity feeling bad about your encroaching age? need to connect with your adult children and think that this will prove to them that you are cool enough to talk to after all these years?

in aid of the charity Blahblahblah. Lots of charities. Why this one?

I would be grateful if you could spare a couple of dollars (or its equivalent) to sponsor me and my sons. I would be grateful if you would spare a couple of $$ or the equivalent to support bringing third world scientists to our meeting. Or students. Or trainees.  Is that more or less valuable than what you are doing? Why? Oh... wait... please DO NOT reply to all to answer

Thank you for reading this Actually, thank you for getting my blood flowing this morning.


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The joy of marvelous colleagues

Mar 06 2015 Published by under collaborators, life

I've spent a few  days  working with four of my most wonderful  and favorite collegues/collaborators. We've been working on a database/NSF grant for the last couple of years. It is not my most favorite research (and hopefully they are not reading this to find that out). But,  working with them has made me care about the science far more than I would have otherwise.

There are lots of reasons we chose what we do. There is a point at which  it just comes down to "this is interesting because X, Y,  Z", where XYZ don't have a meta explanation of their own. Or because it would be cool to cure cancer,  make disabled children walk, understand how mankind  evolved. But why is that interesting?

The impact of collaborators is often underestimated. These folks  have made me think about all sorts of things, and I cannot exactly explain why. They are open and they like to eat cookies.  One went to visit Duke and sent me this picture:20150225_133816_resized




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Things that frost my shorts - reply to all edition and support of junior scientists

Mar 05 2015 Published by under Uncategorized

Continue Reading »

9 responses so far

Not all Republicans are scum

Mar 04 2015 Published by under life

Take this CPP: (its all about the generation)


But the trend is there, the trend is there.


3 responses so far

Things I love

Mar 04 2015 Published by under Uncategorized

I love cooking. I have animal things. Here is one that makes me smile, given to me by a  Japanese colleague:




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Paying for your science - OPM

I just read the original post that prompted a set of tweets that in turn prompted this one from me. Dr. Edward Hind is a postdoc who has spent a lot of his own money doing science. He's also someone who left a more lucrative career to do science. This says he is someone who has looked at the options and made a choice, choosing something he wants that produces less income.

I think the problems, nay implications to the field,  for paying for your own science are significant.  It begins to sound like an initiation fee. Or a system in which one can buy their way to the top. It may exclude people from the lower socioeconomic end of life, and make it much tougher for those in the middle.

But totally unaddressed in Edd's column is who can, let alone the slippery concept of should, pay for these "extras" (which aren't really extra) and where is the money going to come from?

I'm an olde farte. I've been faculty in a variety of departments. They all had money issues. They all had budget shortfall issues. Even the "rich" clinical department had money issues. While that department generated squillions of $$ in clinical income, the med school imposed a "tax" on the clinical departments, in the form of "if you do not bring in X$ in grant overhead, the amount we consider appropriate for your size, you need to give us the difference from your clinical income". Follow the logic and you can feel the leadership being squeezed. Actually, they just made the calculations as to the cost of research faculty and decided on the optimal (in their view) balance of faculty that generated income, and cost them money.

In A&S college departments the budgets were a joke. There is no money in those budgets to cover much of anything, including paper clips and pens, let alone meetings and publishing. When Xeroxing no longer was an issue because of teh interwebtubes, the pathetic allotment for teaching copying disappeared. The A&S Biology department I was in had a small endowment dedicated to graduate students. There were frequent debates as to whether that money should support grad students so they didn't have to teach in the summer and could do field work or whether it should send students to meetings or buy supplies so they could do research. The latter is important in a department where students are their own PI's and not working on their advisor's project.

And there's the problem. What should limited money be spent on? Yup, we pay for professional stuff. But who else should pay for it? The departments? They are making hard decisions about seed money for new hires, money to support grad student research, and how to support junior faculty who didn't get funded at N-3 years counting to tenure, but with a little more money might get enough papers out to get funded next round. They are debating spending money to hire someone to cover teaching (like the postdoc in the department who didn't get a job) for the dude going on sabbatical, so that somebody else doesn't double their teaching load to cover a critical course.

So, you say, the departments should ask for money from the College? Departments are doing this All The Fucking Time. And when they get the money, we just go back to the problems in the paragraph above. The colleges should dictate how the money they give to departments is spent, and  demand that the departments cover the extra costs of everyone from students through postdocs and faculty? Let me tell you how far that would get. Department budgets may be pitiful, but its one of the few tools a chair, a well meaning, hard working chair has to effect change. They are not going to be happy to accept either funded or unfunded mandates from above. This is independent of whether you think that covering a postdoc's meeting costs is a useful and optimal use of any extra money.

Now, Colleges have lots of money, you say. Tuition is going up. But where is that tuition money going? There is a lot of debate about what college budgets are  covering. I've not seen a single clear answer that explains what is happening. I do know that administrative staffing has risen far faster than academic staffing. But plush presidential suites and salaries don't really account for differences in college/university income. There are lots of things colleges spend money. Should they be going to central administration and asking for money? Colleges are doing this All The Fucking Time. Run through the argument above, but with  slightly higher numbers and change "department" to "college" and "college" to "central admin". Do you think Deans would be any more enthusiastic about unfunded mandates on their budgets than chairs? If so, you don't know any Deans. And they are far smoother, by and large, than chairs at arguing their way around budgets.

My current department (basic science in a medical school) has the same concerns and issues. I know some because my current chair (may his health and good attitude last for a very long time) is open and has discussed much of the issues with the faculty. He gives each faculty member an allotment for meetings, memberships and the like. Its on the order of $1000. This year, I spent my money sending two trainees to a national meeting airfare and registration. Yup, I kicked in the rest for them out of my pocket. I didn't go, but if I had I would have paid myself.

Do I want my chair to put in more money to this fund? Nope. This is not an MRU, but an almost MRU. We are not the first choice for really good young people looking for a tenure track job. We've had people scooped out from under us by MRU's that offer 30-60% more seed, even when we meet the request of the candidate. My department has a choice to make: what do we support with the limited money that we can allot? Its a hard decision. We make one choice, and actually some of the faculty don't agree (especially when the hire is in another area than their own). But what investment, and that's what this money is, an investment in the future of the department is going to maximize the life and careers and future of all the constituents? That is not an easy question to answer.

The bottom line comes down to something simple from Econ 101: there are unlimited needs, desires, wants, and limited resources with which to fill those needs. I too would love it someone gave me $20K year to pay for publication and meetings and students and taxis. But I want really good junior faculty in the department more than I want those things.

OPM? Other People's Money - what should pay for all the things we want.

4 responses so far

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