Pairadocs Podcast!

My pet project is taking shape! Presenting The Pairadocs Podcast with Andrew and Derek! Andrew and Derek talk academics/medicine. This week, "What is a Scientist?" Also, cats, porridge, and broken beer bottles. MailBag listener questions about radio waves and birds, "The Crud", and placebo medications! It's not boring, trust us!

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Seminars n' stuff.

I had the pleasure of presenting for our Department's Ph.D. Candidate series and also for the Bioinformatics T32 retreat recently and had someone record my talk at the former location. If you're interested check it out:

Cooking In the Laboratory Part 2: Autoclaved Oncorhynchus mykiss con Brassica sauce.

An Oppressed Graduate Student’s Guide to

Cooking In the Laboratory

The following protocols are intended only as a joke though would likely produce palatable food with only a minimal risk of hazardous contamination leading to injury or death. As always, use proper personal protective equipment (PPE) when dealing with any potentially dangerous chemicals or equipment.

Autoclaved Oncorhynchus mykiss con Brassica sauce

Protocol (Requires individual laboratory optimization) :

1.) Upon capture of a suitable O. mykiss, prepare the organism for consumption by "filleting" the muscle away from spine and removing outer epithelium with cycloid scales intact. This may be performed with a dorsoventral incision posterior to the opurculum on either side, and then sliding the scalpel posteriorly along the spine. Store at 4C until use for up to three days. Discard entrails as biohazardous waste.

2.) Prepare Brassica ovule sauce by crushing appx. 10g of either Brassica juncea or B. nigra ovules using a clean mortar and pestle. Crush ovules until satisfactory disruption of endosperm is achieved. Add 100mg powdered rhizome of tumeric (C. longa) and homogenize mixture until lipids appear to separate from mixture. Mix in 200mg Sodium Chloride and 100mg dehydrated, milled P. nigrum fruits (to taste).

3.) Spread Brassica sauce liberally over the prepared fish fillet (Wear gloves!). Line an autoclave-safe container with heavy-duty aluminum foil. Place the fillet on the foil and cover with another piece of foil. Be sure to mark the container with new autoclave tape to indicate when the item is fully cooked. 

4.) Autoclave on Liquid Cycle (Slow vent) at 115 degrees C and 10 PSI for 15 minutes. Following cycle completion, check to see if autoclave tape was developed and remove the item for consumption. Serve on paper plates to the entire lab. Adjust protocol as necessary. Photograph final product for record keeping. 

5.) Instruct high-school interns to clean up your mess.

Direction

I've been contemplating a way to resurrect this blog. It's a good opportunity for me to write stuff that's not necessarily meant for scientists and share my opinion on various topics. Being able to submit something that won't be destroyed because it's not near-perfect is refreshing, and so I'd like to write more about the things that I know something about. If, in the future, you read a blog and are interested in the topic, leave a comment so I can know to revisit that topic sometime. Perhaps my blog can develop its own personality like Haley's Comic has. 

So far I've contemplated doing a science information series where I take a complex topic and strip it to the bare essentials and introduce that topic to a general audience. This is making the assumption that people out there are actually interested in complex scientific topics. I could probably obsess over what a recombination hotspot is, but I'm not sure many others would find them that fascinating. 

Another idea that would be hard to go wrong with would be a 'how-to' series. I'd introduce one of the many things that I consider to have as a hobby, and basically instruct you how to do something. Examples might include: "How to pull a near-perfect shot of espresso" or "How to tie a basic fishing fly". This would have the advantage of being picture heavy and would probably be more fun for my limited pool of readers. 

Hopefully I can begin to incorporate both of these ideas in future posts. I'll start collecting pictures for an instructable today. Stay tuned!   

My MRTI

Few events are worthy of a blog post.  I felt I should share my notes on my most recent traumatic incident (MRTI {Pronounced "mur-tee" }), my oral comprehensive exam.

Allow me to preface this post by incorporating a word coined by my favorite president of all time, George W. Bush.  I misunderestimated comps. There it is. I went into my MRTI thinking I'd actually get to talk about my projects, what I've done, and what I had planned to do. Instead it was a three hour long examination in how much I didn't know about things that I wasn't working on, all orchestrated by [Redacted] and [Redacted], the devious tag-team dishing out academic retribution (DTTDoAR {Pronounced "Pain Train" because I can}.
I know it's nothing personal, and I admit I have certain deficiencies, but the fact of the matter is that out of three hours, 80% of the presentation was spent on superflous asides that were not directly relevant to what I had done or what I was planning to do. You could ask each of my committee members what I did and what I was going to do (things that were in my presentation) and they would have no idea because of the 30 minute presentation I had prepared, we only got through 1/3rd of my presentation in three hours.

Allow me to tell you about my first slide that we spent 15 minutes on.

Here it is, for example:

Oh, you were expecting some actual content in the first slide were you? You might have been expecting something like, I don't know... words that were worthy of criticism?

The DTTDoAR initiated my MRTI by immediately jumping on this slide. Personally, I thought it was pretty and was a nice model of a Holliday junction which is recombination related and (most importantly) had a blue hue to it and fit into my slideshow.  I did not know that this would be the worst point in my day, heretofore, and simultaneously the best point in the exam. To be honest, it was all down hill from here.

It just got worse. We skipped the first half of the presentation, then went back to it. I'm an evolutionary biologist and the only time the committee was quiet was during the time I was presenting the evolutionary background. 

I guess my project suffers from an identity crisis. It involves a little population genetics, molecular genetics, evolution, and bioinformatics. As such, it's easy to see that I'm a jack of all trades, master of none. If I learned anything from comps, it's this:

1.) Be focused.

If your project spans a lot of directions, pick one and call it your home base. Present everything from that mindset and direction. Don't try to play up the other parts of your project in order to relate it to your committee members or try and pretend that you're a geneticist when you're obviously not. 

2.) Know everything about your slides.

Have a pretty picture on the first slide? Know everything about it, and predict secondary and tertiary questions that could come from it. (e.g. how could this be resolved to form a gene conversion. What ratios would this create in neurospora? What is different about the ratios in neurospora than in yeast.)

3.) Skip the background.

Seriously. If I could re-do this, I'd stick with a little bit of evolutionary background and go directly into my projects, avoiding the secondary and tertiary questions on things that I don't know anything about. If you want your comps to be helpful, go directly into your project and force them as the major topics.

4.) It's an exam, not anything designed to be remotely helpful.

Don't convince yourself that you are presenting your project or talking among friends. Your committee is a ravenous set of pitbulls that haven't been fed in weeks, and you're an injured rabbit that smells like bacon. It's not going to be fair. If you chose your committee to be helpful by incorporating expertise that you don't have, you made a poor decision: they can now quiz you about things that you don't have expertise in. 

All in all, it was definitely my MRTI. Somehow I managed to pass. I think it might have even been a pity-pass because they think I can be chained to a -80 freezer for a few more years and produce something to keep them getting grants. If I wasn't cynical before, this did it. 

Cheers,

Andrew

Ph.D. Candidate 

On Science

<tangent>
So my comprehensive exam is coming up soon.

For most of you that doesn't mean anything, but to those of us silly enough to want to do science for a career, those words strike fear in our heart.  Ph.D. programs typically have two major flaming hoops. The first is an 'easy' qualifying examination designed to see how wide the river flows within the first year or two of the program, and is designed to weed out the bad apples.  Qualifying exams are then often followed by a more intense comprehensive examination that spans a more narrow topic to see 'just how deep the rabbit hole goes'. Except in this case, the rabbit hole they're probing just happens to be your brain. And if it's a mile wide and an inch deep, they'll send you packing with a consolation prize (a Master's) for getting this far (if you're lucky). Let it be known that the University of Iowa sends you out with a pat on the back and a kick in the ass--holding nothing in your hands if you bomb it. As you might imagine, this type of stressor can cause, well, stress.

The combined stresses of flaming hoops in a maze designed by people who never have to actually run the maze (and don't ask the lab rats about it), with marginal pay (considering my undergraduate classmates are doing much better), guidelines that don't actually exist, and the ever present thoughts about doing it all and never getting the job you want eventually wears bright students down. There's abysmally little moral support present in graduate programs, unfortunately. Sure, there's a few advisors that do care, but most of them just don't have time to worry about their students with everything else going on in their lives. And you never quite know just how you're doing... if it's enough,.. where you'll be in a year,... et-cetera.

Y'know, I've often toyed with the grandiose (and completely implausible) idea of starting a university that actually focused on the most stupid thing it could focus on: learning. Now that running a university has become a capitalist venture designed to screw over everyone except the people at the top, it feels like learning and fun have taken a backseat to the backseat (somewhere over in row 9 or 10... err, I think). I'm often left daydreaming about how I would do things differently, steer a university, and design a proper graduate program. I suppose those are topics for later blogs. I guess I need a name for my university first.

</tangent>

Anyhow, that was a tangent if there ever was one. The topic I want to discuss today is the public's view of science. I recently came back from a NSF-sponsored workshop at Duke on "Communicating with the other 99.999% of the world." The main message was pretty simple: give the bottom line first, and toss out the jargon. You would think that this sort of thing would be easy, but it's not. Consider that scientists love science because it's intricate and beautiful, and then realize that 99% of the stuff that we think is cool has to be shaved off in order to get to the bottom line. When my mother asks me what I'm doing, I want to tell her about everything---from lysing cells and pulling out DNA using elegant chemistry to alter the solubility of the desired molecules, to the analysis of data and whether I should do a Spearman's rank or Kindall's tau test. Unfortunately for me, she doesn't care. She wants the bottom line: How does this help me? That too, is hard to answer.

Science moves a lot slower than you would think (at least 99% of the time). The public perception of science ranges from thinking we're actually studying fruit flies (a la Sarah Palin) to wanting to hear, in detail, about the Higg's particle. Actually, that's a good example... Recently physicists have nailed down the so called 'God Particle' to a level that they are convinced they have reasonable evidence of it. If my mother were to ask one of the (many, many) physicist involved in the experiments, "How does this help me?" I presume that they might be befuddled. Certainly confirming the standard model has little impact on my mother's life, yet this is a momentous discovery. The same goes with my work. Sure, the eventual implication would be understanding evolution and finding disease genes, but the immediate impact is minute. Something that's drastically missing from Science education is a sense of history and the impact that even little advances can make. Once we conquer this, I think Sarah Palin might understand that we're not working on fruit flies, but rather trying to understand the simple to understand the complex.

I had my first post-workshop challenge in science communication immediately after I left Duke. On the plane to Iowa I sat beside a guy that could have been from a completely different planet than I. To place this in perspective, this young man had mig-welded a steel bar to the undercarriage of his truck in order to kill raccoons while he was driving along country roads (And then skinning/eating the unfortunate animals).
So there I was, getting asked, "What do you do?" Normally I would go into great detail sharing the exquisite beauty of science, but this fellow had likely barely graduated high school. DNA was likely a tenuous concept for this fellow to understand. So, I tried my best:
"I'm a scientist. Consider a water-hose cranked up to the max, flailing all over the place. There's a prize for the person who can grab the hose at a specific spot, indicated by a red band, but that person is blindfolded. In this analogy, that red band is a disease gene and that's what I want to be able to find. The hose flailing about is our DNA sequence. I'm trying to understand just how the hose flails (recombines) so I can put my hand down at the exact time and place in order to grab that disease gene."

"Wow, that sounds like something."

Me, feeling like a badass, "it is... mostly."

Sure, it leaves out all the intricate glory, but this guy might think about science in a different light now. Who knows, he might even support scientific funding from now on. One can only hope.

End of the year musings

I guess five months is a long time to not update a blog. Most people have probably deemed this blog dead by now, and I wouldn't necessarily disagree with that just yet. I can't quite say if this is just a quiet pop from the fire before the embers cool beyond having the capability of setting alight a new log or if this is a spark of rejuvenation that signals an old engine returning from its year long slumber. In any case, like times before, here I am.

Certainly many things have happened in the last year that are at least of some note. I've officially joined the Comeron Lab and am slowly climbing hand-over-hand toward the next rung of my professional career. I now live in an apartment where I don't want to run outside and scream at the blabbering drunks who think that pulsating low frequencies somehow bring them closer to undergrad Nirvana every weekend. Which also means that I now have my cat living with me--which, is more of a highlight than I'd like to admit, truthfully. I've also been in a relationship with a cultured human being for the entire year too. I hope I've not scared her off after bringing her down to Alabama this holiday season.

Bama is always curious. I returned to my hometown after a year to see that absolutely nothing has changed, save for a new exit off the highway that was designed as a sort of heart bypass,but now is a frivolous plastic surgery since most of the hosiery mills have moved away. Everyone's a little bit fatter, including me, and going on with their lives with a pace that you'd think was predetermined at the point of conception. They're buying houses, getting married, and having children. Now the pattern is so clear. Everyone is doing the same thing that the generation before them did with only minor alterations to the plan. How change comes about in any form is remarkable.

So I suppose I'm trudging on in my own way. Towards some fantastic goal that is sure to impress my friends and family. Some days I yearn to be a cabinet maker or fisherman, producing immediate results with my own hands, cracked and dry after years of work.
I've been so cut off from reality. My work is all about thinking: How can we do this? How does this fit our model of X? What is the purpose of Y? Can we demonstrate that Y affects X? How can I spin this in a way that the government will give me money?  Science is not for the impatient. That's what I learned in 2011. That, and sometimes you've got to stop and appreciate where you've been and where you are. Graduate school has taught me that it's okay to feel stupid and that each person is here for their own specific reason--not just for the same reason I'm here.

It's taken me too long to realize the importance of family and friends. Before, I was so focused on the end that the journey was irrelevant. Anyhow, welcome to 2012. Lets see this as a spark that returns the engine to life.