The Grad Circus

This comic is an homage to my time in graduate school- stimulating and frustrating, a time for development, exploration, and maturation. Pretty much 5 years for me. It’s not strictly autobiographical, though it certainly contains elements from my experience (and my foibles). There were plenty of ways to waste time. On the other hand, if you consider your time as ‘productive’ only when you have your nose to the grindstone you will not end up learning much. Here are some of the things that I didn’t include:

  • I can remember my advisor unlocking the door to HIS office, a bit early in the morning, and finding me playing a first-person shooter on his computer. Ummmm….. oops?
  • Going ‘bowling’ with excess liquid nitrogen. We would take a dewar flask full of the stuff and roll it down the hall. Not much point, but very cool to see.
  • I once scored an entire half of a gigantic sheet cake as ‘free food’. It was left over from a retirement party somewhere in the med school. The admin from our department tipped me off and I retrieved it. Much feasting was had on that day!
  • Many a late night was spent in the lab playing video games with my best friend across the hall. We’d be yelling back and forth at 3 AM then one of us would have to stop the game to collect a sample for a time point.
  • I once found a broken VCR in a dumpster, fixed it, and then sold it for $50- which is like $500 to a grad student. I then proceeded to collect every piece of broken equipment and electronics I could get my hands on- storing it in the lab. I built a rocking platform (retailed at about $600) and repaired several pieces of lab equipment with my haul. However, it really ended up taking up a lot of space.

Graduate school was a great time and one with a lot of freedom that came with the stress. I was lucky to have a great advisor who supported me even when he thought I was goofing off (he did not support me IN the goofing off- he supported me in my career despite that I was goofing off) and a bunch of great friends who I still keep in touch with. There was so much potential in that time- the potential is still there in my career, I just need to take more time to recognize it. And maybe score some more free food too.

 

GradCircus_RedPenBlackPen

On a different note I’m pretty proud of this comic. Some of my previous ideas and concepts have been pretty complicated (see here and here). I’ve thought that I should do an outline sketch first then do a final version with more care. Both of these previous cases I started sketching and just decided to keep it as is. They’re pretty good considering. With this one I actually did sketch out an idea:

 

Initial pen sketch of ideas for the grad circus

Initial pen sketch of ideas for the grad circus

then did a pencil outline of the final

Pencil outlines for the final grad circus. Didn't include details or text.

Pencil outlines for the final grad circus. Didn’t include details or text.

then traced with pen and filled in text and details.

My wife was impressed but said, “maybe for your next one you should do something about a guy that has a full time job and three kids.” Funny. This process did end up taking me about 5 hours (and a few cramped hands) of late evening and weekend time to complete giving me new respect for cartoonists, especially Bil Keane (and now Jeff Keane), whose simple comics look so ‘easy’. These maps are hard to draw!

 

 

 

 

Academic Rejection Training

Following on my previous post about methods to deal with the inevitable, frequent, and necessary instances of academic rejection you’ll face in your career I drew this comic to provide some helpful advice on ways to train for proposal writing. Since the review process generally takes months (well, the delay from the time of submission to the time that you find out is months- not the actual review itself) it’s good to work yourself up to this level slowly. You don’t want to sprain anything in the long haul getting to the proposal rejection stage.

ThreeQuickWays

Please help me with my simple demonstration

I’ve written before about the importance of replicates. Here’s my funny idea of how a scientist might try to carry out this meme of trying to get a picture of yourself holding up a sign passed around the internet to demonstrate the danger of posting stuff to kids/students/etc. And what is up with that anyway? It’s interesting and cool the first few times you see someone do it. But after that it starts to get a *little* bit old.

I am but a poor scientist trying to demonstrate (very confidently) a simple concept.

I am but a poor scientist trying to demonstrate (very confidently) a simple concept.

Nature Transient Findings

You know, I think the glamour publishers could really benefit from a journal to publish these kinds of results. Far less messy and then they won’t get confused with real science. Also, a bonus is that the title of the papers could be already buzzfeed-ready, no editing involved.

Also I’ve officially titled my series of academia-themed comics Red Pen/Black Pen (see previous post for something of an explanation)

Too good to be true or too good to pass up?

Too good to be true or too good to pass up?

This comic was inspired by this wonderful parody, which was circulating awhile back but unfortunately I don’t know proper attribution.

Because you tried really hard for a really long time.

Because you tried really hard for a really long time.

Spaghetti plots? Sashimi? Food-themed Plots for Science!

For whatever reason bioinformaticians and other plot makers like to name (or re-name) plotting methods with food themes. Just saw this paper for “Sashimi plots” to represent alternative isoform expression from RNA-seq data.

Sashimi plots: Quantitative visualization of alternative isoform expression from RNA-seq data

That prompted me to post this from my Tumblr http://scieastereggs.tumblr.com (growing collection of funny bits in scientific publications):

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Spaghetti plots? Lasagne? OK then I can do rigatoni plots

This possibly somewhat satirical paper makes the case for “lasagne plots”, following on the spaghetti plots that are popular in some fields for representing longitudinal data. Lasagne plots are presented as an alternative for large datasets though the authors state: ”To remain consistent with the Italian cuisine-themed spaghetti plot, we refer to heatmaps as ‘lasagna plots.” The remainder of the paper is a pretty straight-on discussion and demonstration of why and when these plots are better than the spaghetti plots.

Lasagna plots: A saucy alternative to spaghetti plots

Bruce J. Swihart, Brian Caffo, Bryan D. James, Matthew Strand, Brian S. Schwartz, Naresh M. Punjabi

Interestingly, a recent paper reimagines heatmaps as “quilt” plots (though less satirically so). This opens whole new doors in the thematic renaming of methods for plotting data.

(h/t @leonidkruglyak)

But, in keeping with the Italian cuisine-themed spaghetti and lasagne plots: Now introducing Rigatoni plots!

(no pasta was harmed in the making of this plot. Well, OK. It was harmed a little)

Need to show outliers? Tasty, tasty outliers? No problem! (thanks @Lewis_Lab)

(capers. They’re capers)

via Spaghetti plots? Lasagne? OK then I can do rigatoni plots.

15 great ways to fool yourself about your results

I’ve written before about how easy it is to fool yourself and some tips on how to avoid it for high-throughput data. Here is a non-exhaustive list of ways you too can join in the fun!

  1. Those results SHOULD be that good. Nearly perfect. It all makes sense.
  2. Our bioinformatics algorithm worked! We put input in and out came output! Yay! Publishing time.
  3. Hey, these are statistically significant results. I don’t need to care about how many different ways I tested to see if SOMETHING was significant about them.
  4. We only need three replicates to come to our conclusions. Really, it’s what everyone does.
  5. These results don’t look all THAT great, but the biological story is VERY compelling.
  6. A pilot study can yield solid conclusions, right?
  7. Biological replicates? Those are pretty much the same as technical replicates, right?
  8. Awesome! Our experiment eliminated one alternate hypothesis. That must mean our hypothesis is TRUE!
  9. Model parameters were chosen based on what produced reasonable output: therefore, they are biologically correct.
  10. The statistics on this comparison just aren’t working out right. If I adjust the background I’m comparing to I can get much better results. That’s legit, right
  11. Repeating the experiment might spoil these good results I’ve got already.
  12. The goal is to get the p-value less than 0.05. End.Of.The.Line. (h/t Siouxsie Wilespvalue_kid_meme
  13. Who, me biased? Bias is for chumps and those not so highly trained in the sciences as an important researcher such as myself. (h/t Siouxsie Wiles)
  14. It doesn’t seem like the right method to use- but that’s the way they did it in this one important paper, so we’re all good. (h/t Siouxsie Wiles)
  15. Sure the results look surprising, and I apparently didn’t write down exactly what I did, and my memory on it’s kinda fuzzy because I did the experiment six months ago, but I must’ve done it THIS way because that’s what would make the most sense.
  16. My PI told me to do this, so it’s the right thing to do. If I doubt that it’s better not to question it since that would make me look dumb.
  17. Don’t sweat the small details- I mean what’s the worst that could happen?

Want to AVOID doing this? Check out my previous post on ways to do robust data analysis and the BioStat Decision Tool from Siouxsie Wiles that will walk you through the process of choosing appropriate statistical analyses for your purposes! Yes, it is JUST THAT EASY!

Feel free to add to this list in the comments. I’m sure there’s a whole gold mine out there. Never a shortage of ways to fool yourself.

 

Dr. Strangefunding or: How I Learned to Stop Worrying and Love the Sequester

I’m currently sitting on a plane heading to Washington DC to give a presentation for the renewal of a large-ish project I’ve recently become involved with. This is significant in that, if it’s renewed, the project will give me additional funding through a critical time. Things are

wallpapers_wile-e-coyote_04_1280dire in research funding right now. For a digest of how dire see the following link. If you’re a research scientist who doesn’t know that I either pity you (because you’re so out of touch) or envy you (because you’re in a position where you just don’t have to worry). But I’m an optimist and optimists like to find the silver
lining of everything, or in this case the green lining (green as in cha-ching, $$$). So here are a collection of thoughts on why this whole sequester, with it’s accompanying 10% reduction in NIH funding, and corresponding decreases in other major funding agencies, just might be a good thing.

  1. The “bottom of the ditch” philosophy: This is my favorite. It goes like this. We’re at the bottom. Things are as bad as they’re likely to get. No, no, no, no, don’t tell me that they could get worse and explain why, I’m an optimist, I won’t believe you. So they’re bad, but we’re still in business and so long as we can scrape by for a little while things will turn around and pretty soon we’ll be rolling in the research dough again. Really. Our luck has to turn around soon, right?
  2. The “culling the herd” philosophy: What doesn’t kill us makes us stronger. Or, more to the point, what doesn’t kill ME makes me stronger- the rest of you all are on your own. And when we emerge from this bloodbath only the strong, fast, and very clever will survive to breed a better stronger generation of research scientists. So either figure out how to be the best or else find someone you can throw to the wolves and hungry lions while you make your escape.
  3. The “honing the elevator speech” philosophy: Previously, in the land of milk and honey and 25% funding levels for NIH R01 grants, you didn’t have to communicate effectively with non-scientists. You didn’t have to communicate all that well with scientists either. Now that we’re in a less favorable funding environment it’s a great time to start honing your outreach skills. Why on earth would ANYONE want to fund the esoteric basic science research that you’re proposing? You don’t just have to convince the reviewers by being really, really, really good at writing a good proposal story, but you also have to justify your existence to the broader public. You may also want to brush up your, “this is why I will make an excellent WalMart employee” elevator talk too, just in case.
  4. The “going back to school” philosophy: This is an excellent time to learn something new to expand your skills and research projects. Think of it as an opportunity. Diversification, without overextending, is really important in any business and is in research as well. Establish new collaborations, investigate new areas, learn new 7395256948_e355c85bc3_bthings- diversify. And you’ll be stronger for it. Will this translate into more $$$ for your research? Maybe not right away, but the investment will pay off.
  5. The “biology not bombs” philosophy: Do you know how much money is spent in this country on defense? It vastly dwarfs research spending by any measure. So one of the outcomes of the sequester is that defense spending will be cut, in a big way. You can debate on whether this is a good thing or bad thing in general, but it’s likely to have an eventual impact on our national priorities. I believe (you can disagree) that we will realize that this isn’t as big of a problem as everyone (or at least a big section of the country) thought it would be. We don’t need to spend a godzillion dollars on the next fighter jet (singular- you want more than one?) And that, in turn will eventually trickle down to a reevaluation of our other priorities. And eventually, it may realign our collective dedication to top-notch, sufficiently funded research in this country. As I said at the start, I’m an optimist.

Feel free to chime in with your optimistic views for research funding. I, for one, say bring on the sequester. I’m ready. I’m not afraid. To quote Major Kong: “Yeeeee-haw. YEEEEEEEEEEEEE-HAAWWWWWWW!!!!”

[2/26/13 9PM Updated RE Ron’s catch below. Yes the first bomb riding clip I had was dubbed in German. That’s what I get for posting from the plane.]

Finally, one last thought.