Excavation

I finished up revising a figure that I’d put together for a paper the other day with such a feeling of finality and satisfaction. Then I realized that I had to do the same thing to two other figures in the same manuscript- and that each one involved a different set of analyses. Each analysis requires me to dig around and figure out where I was and what files I needed to be looking at and even how I’d done the analysis in the first place. It made me feel like I was unearthing a huge pyramid or something- or in a competitive eating contest (as I’ve written about before). So that was the inspiration for today’s comic.

I was giving serious consideration to having the guy have to fight off Nazis, outrun a boulder, and duke it out with a big dude under an airplane after he got the scroll. But I couldn't figure out how to draw faces melting off of the stick figures...

I was giving serious consideration to having the guy have to fight off Nazis, outrun a boulder, and duke it out with a big dude under an airplane after he got the scroll. But I couldn’t figure out how to draw faces melting off of the stick figures…

Asked and answered: Computational Biology Contribution?

So someone asked me this question today: “as a computational biologist,how can you be useful to the world?”. OK so they didn’t ask me, per se, they got to my blog by typing the question into a search engine and I saw this on my WordPress stats page (see bottom of this post). Which made me think- “I don’t know what page they were directed to- but I know I haven’t addressed that specific question before on my blog”. So here’s a quick answer, especially relevant since I’ve been talking with CS people about this at the ACM-BCB meeting the last few days.

As a computational biologist how can you be useful to the world?

  1. Choose your questions carefully. Make sure that the algorithm you’re developing, the software that you’re designing, the fundamental hypothesis that you’re researching is actually one that people (see collaborators, below) are interested in and see the value in. Identify the gaps in the biology that you can address. Don’t build new software for the sake of building new software- generally people (see collaborators) don’t care about a different way to do the same thing, even if it’s moderately better than the old way.
  2. Collaborate with biologists, clinicians, public health experts, etc. Go to the people who have the problems. What they can offer you is focus on important problems that will improve the impact of your research (you want NIH funding? You HAVE to have impact and probably collaborators). What you can give them is a solution to a problem that they are actually facing. Approach the relationship with care though since this is where the language barrier between fields can be very difficult (a forthcoming post from me in the near future on this). Make sure that you interact with these collaborators during the process- that way you don’t go off and do something completely different than what they had in their heads.
  3. In research be rigorous. The last thing that anyone in any discipline needs is a study that has not considered validation, generalizability, statistical significance, or having a gold-standard or reasonable facsimile thereof to compare to. Consider collaborating with a statistician to at least run your ideas by- they can be very helpful, or a senior computational biologist mentor.
  4. In software development be thoughtful. Consider robustness of your code- have you tested it extensively? How will average users (see collaborators, above) be able to get their data into it? How will average users be able to interpret the results of your methods? Put effort into working with those collaborators to define the user interface and user experience. They don’t (to a point) care about execution times as long as it finishes in a reasonable amount of time (have your software estimate time to completion and display it) and it gives good results. They do care if they can’t use it (or rather they completely don’t care and will stop working with you on the spot).
  5. Sometimes people don’t know what they need until they see it. This is a tip for at least 10th level computational biologists (to make a D&D analogy). This was a tenet of Steve Jobs of Apple and I believe it to be true. Sometimes, someone with passion and skill has to break new ground and do something that no one is asking them to do but that they will LOVE and won’t know how they lived without it. IT IS HIGHLY LIKELY THAT THIS IS NOT YOU. This is a pretty sure route to madness, wearing a tin hat, and spouting “you fools! you’ll never understand my GENIUS”- keep that in mind.
  6. For a computational biologist with some experience make sure that you pass it along. Attend conferences where there are likely to be younger faculty/staff members, students, and post-docs. Comment on their posters and engage. When possible suggest or make connections with collaborators (see above) for them. Question them closely on the four points above- just asking the questions may be an effective way of conveying importance. Organize sessions at these conferences. In your own institution be an accessible and engaged mentor. This has the most potential to increase your impact on the world. It’s true.

Next week: “pathogens found in confectionary” (OK- probably not going to get to that one, but interesting anyway)

People be searchin'

People be searchin’

Gravity Alternate Ending

This joke’s a SPOILER (at least in part) for the movie Gravity. I liked the movie a lot, thought it was an exciting drama/survival adventure. My wife wasn’t sold:

Her: “It’s too much like that movie with Tom Hanks”

Me: “Oh sure, Apollo 13”

Her: “No… the one with the volleyball”

Me: “Oh.”

She’s right, of course. It shares something in common with Castaway.

Anyway- here’s my idea for an alternate ending. You know, to sci-fi-it up a bit…

 

GravityAlternateEnding

The Compliment Cascade

I got my PhD in Immunology and Microbiology, so I really know what I’m talking about. This is how the complement system really works- a lot more positive, and a lot less cutting and cleaving than is commonly thought (see here for the real thing).

And, yes, I realize I didn't complete the cascade fully (or include alternate pathways). But I felt the joke had (more than) run it's course by the third panel.

And, yes, I realize I didn’t complete the cascade fully (or include alternate pathways). But I felt the joke had (more than) run it’s course by the third panel.

The Dawn of Peer Review

Elditor summary:

Ugck-ptha, et al. report the development of “fire”, a hot, dangerous, yellow effect that is caused by repeatedly knocking two stones together. They claim that the collision of the stones causes a small sky-anger that is used to seed grass and small sticks with the fire. This then grows quickly and requires larger sticks to maintain. The fire can be maintained in this state indefinitely, provided that there are fresh sticks. They state that this will revolutionize the consumption of food, defenses against dangerous animals, and even provide light to our caves.

Reviewer 1: Urgh! Fire good. Make good meat.

Reviewer 2: Fire ouch. Pretty. Nice fire. Good fire.

Reviewer 3: An interesting finding to be sure. However, I am highly skeptical of the novelty of this “discovery” as Grok, et al. reported the finding that two stones knocked together could produce sky-anger five summers ago (I note that this seminal work was not mentioned by Ugck-ptha, et al. in their presentation). This seems, at best, to be a modest advancement on his previous work. Also, sky-anger occurs naturally during great storm times- why would we need to create it ourselves? I feel that fire would not be of significant interest to our tribe. Possibly this finding would be more suitable if presented to the smaller Krogth clan across the long river?

Additional concerns are listed here.

  1. The results should be repeated using alternate methods of creating sky-anger besides stones. Possibly animal skulls, goat wool, or sweet berries would work better?
  2. The dangers with the unregulated expansion of fire are particularly disturbing and do not seem to be considered by Ugck-ptha, et al. in the slightest. It appears that this study has had no ethical review by tribe elders.
  3. The color of this fire is jarring. Perhaps trying something that is more soothing, such as blue or green, would improve the utility of this fire?
  4. The significance of this finding seems marginal. Though it does indeed yield blackened meat that is hot to the touch, no one eats this kind of meat.
  5. There were also numerous errors in the presentation. Ugck-ptha, et al. repeatedly referred to sky-anger as “fiery sky light”, the color of the stones used was not described at all, “ugg-umph” was used more than twenty times during the presentation, and “clovey grass” was never clearly defined.
With a h/t to Douglas Adams

With a h/t to Douglas Adams

Career Strategy

Including this on my actual CV could be a problem though...

Including this on my actual CV could be a problem though…

I Tweeted this last week as a brilliant idea for a career move.

The largest barrier I see to this actually working is that it will be difficult to include it on my  printed CV. And have the same effect at least. I’m working on it. Also it has a similar bad taste as the “research” group that bought their own journal to publish their ridiculous paper on Sasquatch DNA.

Turns out, of course, that I’d been beaten to the idea by actual publishers:  

Screen Shot 2014-09-02 at 9.30.18 AM home_cover Screen Shot 2014-09-02 at 9.32.46 AM

As pointed out:

I think I’ve still got something novel with the whole “Other High Impact” journal idea. *BRILLIANT!!!*