Biology is Magic

Over the past week, I’ve come to the conclusion that Biology is actually just magic in disguise. Sure, it’s all generally explicable using scientific facts. And there aren’t any wands (unless you count pipettes), or robes (unless you count lab coats), or magic spells that have to be followed to the letter or you risk everything going horribly wrong (unless you count protocols...). Basically, even if biology isn’t really magic, the parallels are often hard to ignore. At least when you’re willfully seeking them out for the sake of justifying your metaphor usage. :P

The reason that I’m justifying this particular metaphor this week is that I followed the same protocol, trying to do the same thing, all last week, and I got wildly different results. Specifically, I was trying to extract DNA in order to mess with it a bit and insert a ‘lesion’, which in this case is just an incorrect base pair. DNA relies on the fact that all base pairs have specific pairings (A with T and G with C) and when one of those pairings is incorrect, cells will go through one of various processes to fix the incorrect pairing. When done according to the protocol, a ‘pellet’ (basically a little solid white bit at the bottom of the tube, as compared with the aqueous contents in the rest of the tube) should form after you centrifuge the samples (spin them really hard and really fast) for a long enough period of time. The problem was that even after centrifuging my samples for plenty of time, no pellet was visible.

The first time I went through the protocol with my grad student supervising, everything went perfectly. The pellets showed up when they were supposed to, and although my DNA yield (the concentration of DNA that you’ve extracted at the end of the protocol) was a bit low, it was pretty decent for only having run through the protocol once. As a result, my grad student and I decided that it would be fine for me to do the protocol again the next day, but on my own this time, while he worked on other things.

Everything seemed to go pretty well this time, until I got to measuring the DNA yield. It was decidedly low. We decided that something had probably gone wrong, but neither of us were able to work out what it was, so it was decided that I would just try again the next day. I went through the protocol again, but this time there weren’t any visible pellets, even after the centrifuging steps. Over the summer, this sometimes happened when I was extracting DNA to genotype mice, so I continued with the protocol under the assumption that there would still be DNA in my samples. And there was, but the yield was still fairly low, so we decided that my grad student and I would run through the protocol together the next day.

Upon doing so, we discovered that I was doing the protocol in the exact same way he was, but his samples showed pellets after centrifuging, and only one of mine did (since all three of the tubes are the same sample, just split into three tubes so that everything you need to add to get the DNA to come out of solution will fit, this made literally no sense). We decided to carry on with the protocol, and see what happened. The DNA yield wasn’t overly low, but we decided to both run through it again the next day, correcting any little things that might possibly have been the problem. Surprisingly, we again found that his samples all showed pellets after centrifuging, but only one of mine did. However, neither of us could come up with any reasonable explanation for this, since we were doing everything in the same way, right down to how our samples were being mixed.

Since neither of us could see what I was doing wrong (if anything... which seemed fairly unlikely at this point), we decided that my grad student would go back to the other things he was doing, and I would try the protocol again the next day. This time, only one pellet showed up again after the first centrifugation. However, in the following two centrifugation steps, which are meant to ‘wash’ the pellet (essentially just get rid of any undesired chemicals) the remaining pellets magically appeared. We still don’t know what’s up with what I’m doing, but the pellets are at least appearing now, which is a plus.

Anyway, this was all a long story to tell you why I think biology is rather magical. Although there’s pretty much no reason some of this stuff should be happening, it is. And honestly, the first person to come up with the ‘wash’ steps probably didn’t have too much justification for doing so, other than that maybe washing twice with 70% ethanol will help get only DNA in the final sample. There are several version of the protocol we’re using online, and some of them only call for one wash step, while some call for three. Two washes is kind of arbitrary, but we’ve seen that it works, so we’re sticking to it.

There are other cases in which biology is pretty magical. Basically any time you’re working with DNA or RNA, you stand a chance of being told ‘Don’t look at it the wrong way.’ DNA and RNA are fragile molecules, so apparently sending them bad vibes will decrease the chances of your protocol working. This isn’t just something that my lab says either- I’ve seen it said on a few protocol advice websites for biologists, and several of my friends who work in other labs have told me that they’ve been told the same thing. There’s no reason for looking at your samples wrong to screw up the experiment. But biology is magic, so even inconsequential things can cause problems.

When you don’t know the biological reasons behind why things work, it’s easy to look at something and call it magic. I’m pretty sure I thought cold medicine was magical when I was younger, solely because I didn’t know why it worked. The funny thing is, even when you do understand the biological reasons for things, they still seem pretty magical. I know I harp on this example all the time, but scientists have literally stripped all of the cells out of a heart, leaving only the extracellular matrix, and repopulated that matrix with stem cells, creating a fully functional heart. I understand the principles behind that, but it still strikes me as incredibly amazing.

Growing up on fictional stories like I did lends itself to attributing amazing things to magic. The vast majority of books I read when I was younger had some sort of magic in them, whether it was spells and potions like the Harry Potter series, or talking animals like The Chronicles of Narnia. While growing up has made it a bit harder to believe those stories as much as I once did, it’s also allowed me to find new instances of magic. Which is, I think, one of the things that makes growing up special. And that’s why, even though I understand so many more biological principles than I once did, I’ll probably always maintain that Biology is Magic.