Revisions on the monkey

Well, I did it. A day late, but whatever - it's off. I finished the revisions on the monkey and I've sent it off to both of my PhD supervisors.

So I'll just sit back and wait to hear from General Solution Guru, who always has excellent comments and thanks to her the work is far more sophisticated than I would have been able to do on my own.

I really hope that we can submit this baby soon. I'm dying for that Jack Daniels.

Science is a Gaussian distribution away from truth.

Today I had a very interesting conversation with YoungEnthusiasticScientist (YES) over lunch. I was asking him some statistical questions because I was having trouble getting my head around how to do certain things. And then our conversation veered to the dreaded question, had my paper gone out for review? Have I submitted TheMonkey yet?

I sheepishly said 'no.' But then explained I didn't want to submit something that I didn't think wasn't truthful. How could I submit something that wasn't accurate to my best ability, wouldn't that be lying?

His reply, "Then you'll never be able to submit it." Gesturing with his hands, he drew a line up in the air, "Truth is up here." Then he drew an imaginary Gaussian distribution below this imaginary line. "And all of us that do science, we're down here. Science is an approximation of the truth. I have papers that I submitted years ago that I totally disagree with the conclusions now. That's how science progresses. You do shit - find out its wrong - change how you do shit and do some more shit - then find out that it's wrong, etc. Science is recursive."

I answered, "But won't the reviewers reject it if they find problems? And my PhD supervisor, GeneralSolutionGuru says you should be your own worst critic."

YES responded with, "Reviewers will often reject something when they can feel clever. If they read your paper and find something that they can go, 'aha, now I feel clever' your paper will be rejected. So don't let them feel clever, just put in all the caveats and then send the thing out!"

Okay, YoungEnthusiasticScientist. I will. I know I have a problem called perfectionism, but I can do this. Despite the personal shit that is currently happening, I will have this paper to GSG by the end of next week. I can let go.

Reflections on a successful transplant.

I'm back in SmallTown, America after a week long visit to BigCity, Canada. The reason I went to the BigCity was to help out some colleagues with an experiment we started while I was still living there. This is not my first attempt at a collaboration and I really hope it does not go the way of my two other 'collaborations'. Those ones ended badly for me. In the first case, I was brought into a postdoc's office and told that I was being taken off the paper because she had decided it wasn't worth it to her to have too many authors. Myself and one other grad student were "summarily dismissed" after we contributed a great deal of time and energy collecting data and help with building a model.

So when we started this experiment, I have to say I was a little uncertain and hesistant about contributing time. I know that it is often the case where you start a bunch projects with people, some will go nowhere, while others will bloom. My past experience suggests that the ones which are likely to end badly (where someone is removed from authorship, despite the contribution of data) may have more to do with the self-serving motivations of the people involved.

Right now, I'm working with two people who do not let ambition dictate how they operate in their professional relationships. The lead on this project, LivingtheScottishLife (LSL), is respectful and keeps me involved in the decision making process, despite the fact that I live so far away. I really appreciate this and so I do my best to participate fully and help out as much as I can. This in my mind did not happen in the two other cases - I was not seen as a colleague but merely a doorstep for someone else's career.

The experiment was so involved that while in the BigCity, I spent most of my days transplanting many little seedlings, from a shared space in a tiny little pot into their own larger pots. A lovely metaphor for what has occurred in my own life. I have moved from a large university so crowded with students all competiting for space and recognition to a small university with tons of space to allow this little seedling to blossom. It was ironic that I did all of this work in LargeUniversityinCanada's (LUC) greenhouse but it gave me time to reflect on my own transplantation.

One thing I thought about was how my interaction with GeneralSolutionGuru (my PhD supervisor) was different than that of the interactions I have with Dr.Add'emUp (my postdoc supervisor). Both supervisors are incredibly smart and supportive, but when I talk with Dr Add'emUp I feel like a colleague.

I am sure this has more to do with my confidence.

It was good to return to LUC having spent time away in a small place where the emphasis is on collaboration because I now understand that despite the strong academic training, I was finished my training at LUC.

Even though SmallUniversity is small, the people here have big hearts and there is plenty of space for me grow.

The Value of Science in Canada

Today I tried to work on revising my FNP, but I found myself incredibly distracted and unfocused. I've received comments from GeneralSolutionGuru and as per usual she has given excellent and detailed criticism. It's amazing, I thought I had nailed the manuscript but as I go through her comments, I think 'why didn't I pick that up', 'oh my god did I really do that' and 'she must think I was on crack when I did that'? And on and on, it goes.

The whole sobbing at work thing is tiring plus I think my officemate, who doesn't really speak English, must think I'm insane. Not the most poetic thing to say but - death sucks.

So as a distraction, I've decided to blog about a couple of recent emails I've received from friends that show that the scientific community in Canada is frustrated and fearful at the conservative government's treatment of fundamental scientific research.

But really is this surprising?

Stephen Harper (the Prime Minister of Canada) is, as far as I'm concerned, has an underlying ideology that he weasels into every policy. While I may be a granola eating birkie-wearing tree hugger, Harper is a neo-con who lives and dies by the market. He won't listen to hard-done-by stories of the 'little people' and his natural inclination is toward rigid conservative policies. Stephen Harper's closest advisor (Tom Flanagan) believes in the teachings of Leo Strauss, a man who taught that people "are too stupid to make informed decisions about their political affairs. Elite philosophers must decide on affairs of state for us." Strauss also believed that the ruling elite should hide the truth from the public -- Strauss's "noble lie" -- in order to protect the citizens from themselves.

The comparison between Harper and Bush is stark and explains why Canadian scientists are fearful about the future of science. For more details on the Harper-Bush comparison see this article.

It is only because Bush had his head up his axis of evil for 8 years that the US is ready for whatever change comes their way. It means that Obama is given quite a bit of leeway. It's why he can return science to its rightful place and increase the presence of science in policy-making. In his 2009 Budget Obama stated, "investments in science and technology foster economic growth, create millions of high-tech, high-wage jobs that allow American workers to lead the global economy.” Thus, Obama has committed $7 billion to NSF and $10 billion to NIH.

Furthermore, Obama believes in higher education. He has proposed to increase the maximum Pell Grant for low-income college students to $5,550, making it part of the federal government's mandatory annual budget. This is quite an unusual move because it will protect the funding from political and budgetary pressures and link grant increases for students to inflation. Today Pell Grants cover only 35% of the cost of attending college, 30 years ago it covered 77%.

Lastly Obama has selected a science and technology administration consisting of Nobel prize winning Steven Chu, a marine biologist, Jane Lubchenco, and a Harvard physicist John P. Holdren.


Let's look at the Canadian plan.



Stephen Harper has cut the base budgets of three science councils: CIHR, NSERC and SSHRC by $87.2 million over three years. In his budget, Harper suggests that this reduction in research support will be shifted to fund graduate scholarships (500 doctoral fellowships at $35000 each and 1000 one-time Master's level grants valued at $17, 100 each). This increase in scholarships is temporary and will revert back to previous levels after 2 years but the reduction in funding to the tri-councils is permanent. While I think it is important to have strong funding for graduate students, it seems that the reason most of us choose a particular school is because of the research program. To maintain solid research programs funding needs to be stable. It is also perfectly clear to anyone with half a mind that some of the biggest labs employ up to 50 people if not more.

The second problem with this type of funding is it accents an already present hierarchy among graduate students. Those with strong funding sources don't have to TA or find other means of support and hence can focus on the research and finish their degree in a timely manner. This advantage is cumulative. Good funding at the Phd level translates to funding at the post-doc level and so on. I realize life isn't fair. But must we foster inequality?

Finally, restricting funding for Master's students to a single year de-values and marginalizes the degree. A MSc. is an important stepping stone for those students who aren't sure that they want to pursue a scientific career. Click here to find out why 1-year of funding is simply not enough for a Masters.

As if it wasn't enough to have muzzled Environment Canada's scientists and removed the independent science advisor, the Harper government continues to show its disregard for science.

In a 2003 speech that Harper gave to Civitas (a network of Canadian neoconservative and libertarian academics, politicians, journalists), he said that the state should take a more activist role in policing social norms and values. Now in the Budget 2009, the Government of Canada wants to allocate $17.5 million over three years to Social Sciences and Humanities Research Council (SSHRC) to fund an additional graduate work “focused on business-related degrees.”

Then at a meeting between David Robinson, associate executive director of the Canadian Association of University Teachers and Gary Goodyear, Minister of Science things erupted. From a Globe and Mail article,

"The minister was very angry," said David Robinson, associate executive director of CAUT. "He was raising his voice and pointing his finger ... He said everyone loves their [federal budget] and we said, 'A lot of our members don't love it'... and he said, 'That's because you're lying to them, misleading them.' "

(Misleading the public is a Harper speciality and harkens back to his Straussian belief in the "noble lie." )


The most obvious way Harper has shown his disregard for science is to hire a chiropractor as the Minister of Science and Technology, Gary Goodyear. My mom always said chiropractor's were quacks. And she was always right.

It's no coincidence that there is a resemblance between the new Canadian emperor, Stephen Harper and Homer.

The monkey is out the door.

This video says it all. Now, I await comments, but the hard part is mostly done!

Kicking The Monkey - Update

I haven't been blogging lately because I'm so close to booting that monkey out the door. How close you ask?
<<<--- This close.

There is definitely a lot to blog about when I get back. The first will be the February carnival on diversity. And then watch out...

See you folks soon!!

Update on Kicking the Monkey

Just an update for those of interested in how my progress is coming on kicking that monkey. My R program continues on its grid search for the meaning of life. Sheesh! I have 3000 parameters left to go. I'm hoping that this will be done at the end of the week at which point I can move on to doing my sensitivity analysis. At least I'm making progress, albeit slow.

Kicking The Monkey = PhD.

Inspired by Dr. Jekyll and Mrs. Hyde's post, I've decided to give some time to thinking about the ghost of christmas past. Forget the ghosts of present and future because the one that I'm irritated by is the ghost of the past.

Stupid monkey. Stop taunting me.


I am, of course, referring to manuscripts left over from my thesis, oh so long ago.

Despite my best efforts (okay not best, but at the very least okay efforts) I can't seem to motivate myself to return to those yet-to-be-published-PhD-manuscripts.

The work is good and at least one manuscript is so incredibly close to being submitted.

Every time I sit down to start the process, it turns out the house needs cleaning, oh I should really go and do that lab work, yeah wasn't there a blog I meant to write?, I should really shovel the driveway...

You name the excuse and I've whored myself to it.

Enough is enough. So before New Year's Eve arrives and everyone goes into a spiral towards Resolutions, I shall attempt to kick the monkey first.

Plus at coffee last week LookAlike said she'd kick my ass if I didn't get on this already.

So to get the monkey off my back, I propose to:

1. Find and organize the old data files.

2. Look over the R script sent to me by the R Wizard in my former lab, currently a PhD student who I fondly call, Westgrid.

3. Run a grid search on my data, to find "the meaning of the universe".

4. Run a simulation to test how age structure affects "the meaning of the universe."

5. Rewrite the main text to include the new numbers and adjust the interpretation.

6. Rewrite the SupMat to reflect the updated analysis.

7. Make the appropriate figures and tables with the new information.

8. Send the polished manuscript to Aspergers and GeneralSolutionGuru, my former PhD supervisors.

9. Revise. (I know this will happen because GeneralSolutionGuru always has revisions.)

10. Submit the FNP.

11. Have a good stiff drink from a bottle of Jack Daniels.

That felt good.

I've given myself a January 31st deadline to submit the manuscript to the former PhD supervisors.

Watch me kick that monkey. Kick, kick...no not that part of my ego...wait I'm sorry Mr. Monkey...ahhhh.....

Stinking PhD - get published already.

I'm feeling really frustrated right now.

Right now I am desperately trying to finish up some manuscripts from my PhD. But I can't figure out why I'm having such a hard time converting my efforts into something productive (ie. pubs). I've been working on this one analysis for what feels like ages and it's essentially preventing me from getting this work published.

I feel quite alone in this endeavour.

I know the project is a good piece of science and I know that I'm not stupid - but right now I feel incredibly dumb and like shelving the stinking PhD forever.

AHHHHHHH!!!