Making a super villain

I’ve written about Reviewer 3 before (here, here, here, and here). Somehow the third reviewer has come to embody the capriciousness (and sometimes meanness) of the anonymous peer review process. Note that I believe in the peer review process, but am a realist about what it means and what it accomplishes. It doesn’t mean that every paper passing peer review is perfect and it doesn’t mean that every peer reviewer is doing a great job of reviewing.

When I’m a reviewer I see the peer review process through the lens of the line from Spiderman (Stan Lee), “with great power comes great responsibility”. I strive to put as much effort in to each paper I review as I would expect and want from the reviewers who review my papers. Sometimes that means that I don’t get my reviews back exactly on time- but better that than a crappy, half-thought-through review. I’m not sure that I always succeed. Sometimes I think that I may have missed points made by the authors, or I may have the wrong idea about an approach or result. However, if I’ve done a good job of trying to get it right the peer review process is working.


I, for one, welcome our midichlorian overlords


STAR WARS is really just a treatise on microbial evolution and the concept of the selfish gene. See below for more details.






So here’s the idea. The concept of midichlorians was introduced in the prequels. They are “a microscopic lifeform that reside within all living cells and communicate with the Force”. So essentially mitochondria, but powered by the Force. Han Solo has a great quote in episode IV,

Kid, I’ve flown from one side of this galaxy to the other, and I’ve seen a lot of strange stuff, but I’ve never seen *anything* to make me believe that there’s one all-powerful Force controlling everything. ‘Cause no mystical energy field controls *my* destiny. – Han Solo

But with midichlorians you now have a genetically discrete entity that is the sole communication with the powerful Force. The midichlorians want, in an evolutionary sense, to preserve and continue their lineage- they are ‘selfish’. So it stands to reason that they would have a say in what was going on with their hosts. A ‘host’ is simply a very large (relatively speaking) machine to enact the plans of the midichlorians. Of course. A kind of large biosuit for battle. So it’s amusing to think of them controlling all the battles like they’re playing video games.

Incidentally, this is not my first Star Wars inspired comic. That would be here.

More Science Caution Signs

You asked for it (you don’t remember? Well, you did) so you got it. More science caution signs.

This time I had some help. See the contributions of ideas from:

And there were some other ideas too that I just haven’t put into a visual representation yet- so there may be another installment of these important warning signs in the future.



Academic Halloween Costumes

It’s that time of year. You’ve been invited to a costume party and now must decide: what will you dress up as? Well, I’ve assembled some of the BEST Halloween costume ideas for overworked, stressed out, over thinking academics right here. If you have further suggestions please Tweet them with the hashtag #academiccostumes.



I’ve posted before about some of my organizational approaches (and attempts at it) but it can sometimes be impossible not to get overwhelmed and busy. Being busy on multiple tasks, with multiple deadlines can be a killer, but sometimes it crystallizes a resolve to move some of those items off your todo list and you increase your overall effectiveness (you know, less Twitter and blogging and comic-making and stuff). I’ve also seen people who seem to make it a part of their academic persona to be perpetually too busy. This seems to be considered a status symbol (often times mostly by the person being so busy). The key to busy-ness and keeping your head above water (and the seals at bay) is balance. Make sure to keep perspective about what you’re doing and know that often (maybe always) banging your head against the same task for hours on end is counterproductive.

Anyway, here’s a handy tool to help you assess your level of busy-ness, fresh from the RedPen/BlackPen labs.


Phenomenal science powers!

So you toil for 4+ years in graduate school, 4+ years as a post-doc, land your first academic gig. Now you get to do all this awesome science, right? Well, sorta…

Oy! 10,000 years in the cave of graduate school will give you SUCH a crook in the neck!

Oy! 10,000 years in the cave of graduate school will give you SUCH a crook in the neck!

Best Practices


This comic is inspired, not by real interactions I’ve had with developers (no developer has ever volunteered to get within 20 paces of my code), but rather by discussions online on the importance of ‘proper’ coding. Here’s a comic from xkcd which has a different point:

My reaction to this– as a bench biology-trained computational biologist who has never taken a computer programming class– is “who cares?” If it works, really, who cares?

Sure, there are very good reasons for standard programming practices, standards, and clean, efficient code. Even in bioinformatics (or especially so). These would be almost exclusively applicable to approaches that you’ve had quite a bit of experience with working out the bugs, figuring out how it works with the underlying data, making sure that it’s actually useful in terms of the biology. This is at least 75% of my job. I try and discard many approaches for any particular problem I’m working on. It’s important to have a record of these attempts, but this code doesn’t have to be clean or efficient. There are exceptions to this, such as when you have code that takes a loooong time to run even once, you probably want to make that as efficient as you can. The vast majority of the things I do- even with large amounts of data- I can determine if they’re working or not in a reasonable amount of time using inefficient code (anything written in R, for example).

The other part, where good coding is important, is when you want the code to be usable by other people. This is an incredibly important part of computational biology and I’m not trying to downplay its importance here. This is when you’re relatively certain that the code will be looked at and/or used by other people in your own group and when you publish or release the code to a wider audience.

For further reading into this subject here’s a post from Byte Size Biology that covers some great ideas for writing *research* code. And here is some dissenting opinion from Living in and Ivory Basement touting the importance of good programming practices (note- I don’t disagree, but do believe that at least 75% of the coding I do should not have such a high bar- not necessary and I’d never get anything done) . Finally, here are some of my thoughts on how coding really follows the scientific method.

Writing Yourself Into A Corner

I’ve been fascinated with the idea of investment, and how it can color your thoughts, feelings, and opinions about something. Not the monetary sense of the word (though probably that too) but the emotional and intellectual sense of the word. If you’ve ever been in a bad relationship you might have fallen prey to this reasoning- “I’m in this relationship and I’m not getting out because reasons so admitting that’s it’s absolutely terrible for me is unthinkable so I’m going to pretend like it’s not and I’m going to believe that it’s not and I’m going to tell everyone that I’m doing great”. I really believe this can be a motivating factor for a big chunk of human behavior.

And it’s certainly a problem in science. When you become too invested in an idea or an approach or a tool- that is, you’ve spent a considerable amount of time researching or promoting it- it can be very difficult to distance yourself from that thing and admit that you might have it wrong. That would be unthinkable.

Sometimes this investment pitfall is contagious. If you’re on a project working together with others for common goals the problem of investment can become more complicated. That is, if I’ve said something, and some amount of group effort has been put into this idea, but it turns out I was wrong about it, it can be difficult to raise that to the rest of the group. Though, I note, that it is really imperative that it is raised. This can become more difficult if the ideas or preliminary results you’ve put forward become part of the project- through presentations made by others or through further investment of project resources to follow up on these leads.

I think this sometimes happens when you’re writing an early draft of a document- though the effect can be more subtle here. If you write words down and put out ideas that are generally sound and on-point it can be hard for you, or others who may edit the paper after you, to erase these. More importantly a first draft, no matter how preliminary or draft-y, can establish an organization that can be hard to break. Clearly if there are parts that really don’t work, or don’t fit, or aren’t true, they can be removed fairly easily. The bigger problems lie in those parts that are *pretty good*. I’ve looked back at my own preliminary drafts and realized (after a whole lot of work trying to get things to fit) that the initial overall organization was somehow wrong- and that I really need to rip it all apart and start over, at least in terms of the organization. I’ve also seen this in other people’s work, where something just doesn’t seem right about a paper, but I really can’t place my finger on what- at least not without a bunch of effort.

Does this mean that you should very carefully plan out your preliminary drafts? Not at all. That’s essentially the route to complete gridlock and non-productivity. Rather, you should be aware of this problem and be willing to be flexible. Realize that what you put down on the paper for the first draft (or early versions of analysis) is subject to change- and make others you are working with aware of this explicitly (simply labeling something as “preliminary analysis” or “rough draft” isn’t explicit enough). And don’t be afraid to back away from it if it’s not working out. It’s much better if that happens earlier in the process than later- that is, it’s better to completely tear down a final draft of a paper than to have reviewers completely miss the point of what you’re trying to say after you’ve submitted it.