The Futile Cycle

All right, time to settle a vitally important issue in lab science.

I’ve heard people pronounce “autophagy” as both AW-tuh-fey-jee and uh-TAW-fuh-jee. Clearly, it should be pronounced as the former, like any normal person. The latter pronunciation makes the speaker sound pretentious and silly, whereas the former makes him or her sound practical and to the point, like a serious scientist.

Don’t come quoting to me from the dictionary, either. Do you say “HA-rass” for “harASS”, though that’s the way it is in the dictionary? No, of course not. Because you’d sound like a silly fop otherwise.

Besides, everyone pronounces “autophagosome” as AW-tuh-FA-go-some, and not uh-TAW-fuh-go-some. And no one says uh-TAW-mow-beel for “automobile.”

So there. Those who say “uh-TAW-fuh-jee” will be teased mercilessly.

I’ve found a bunch of tools recently that have made organizing my life a lot easier, especially with integrating labwork into the rest of my life.

First up is Remember the Milk, which is a free, online to-do list manager. It’s simple, but very useful. I can create multiple lists, tag each list item, and create smart lists based on searches. It’s all done very well, including lots of AJAX-y goodness and keyboard shortcuts to boot. For FireFox users, it has nice integration with Google Gears for offline access. It also integrates into Gmail and Google Calendar, though I’ve used those features less. The only caveat I have with RTM is that I wish its keyboard shortcuts mimicked those in Gmail. Gmail’s shortcuts seem much more intuitive than RTM’s, such as using “x” instead of “i” to select or deselect items.

Having an online tool is really handy, as sometimes I don’t have my computer with me, especially in lab. My To-Do list, however, is only an internet connection’s away.

Next is Gmail. Yes, many people use Gmail, but I especially like to use Gmail to shuttle little bits of data back and forth as attachments on drafts of letters to myself. Very handy! And Gmail’s recent introduction of IMAP has made it a lot easier to keep track of my email from both my home computer as well as a lab computer.

Another amazingly useful tool is Google Calendar. It’s very handy to be able to check my schedule from any computer, but the main problem is that I like the way iCal is integrated into the rest of my system! It picks up dates and times from email read in Apple Mail, it integrates with the Address Book, and alerts are simple to create, making it so much easier to manage my time at my home computer.

So I use BusySync. The 2.0 beta (as I write this) includes Google Calendar synchronization, which is an absolute godsend. The synchronization is seamless!

RTM combined with Google Calendar + BusySync + iCal is a killer combination for me; I can keep track of experiments, time points, appointments, meetings, seminars, classes, and even the rest of my life regardless of what computer I’m on! And now that I use an electronic lab notebook published online (though under a password), I can access data and procedures from home, too, so that I can plan out experiments or process data and record it wherever I am. It’s glorious!

Alas, the only thing I can’t do is pipette my reactions or maintain cell culture from home…Hey Honda, any chance you might come out with an ASIMO Laboratory Rat model?

I’ve been thinking a lot lately about picking a lab for my thesis, and part of that has involved thinking about what kind of organism I want to do research on.

Of course, I have a strong interest in medicine, so perhaps my basic science research should be on a human-like system, such as on cultured human cells or human cancer cells, which are pretty common. When I first started learning biology, I thought to myself, “If mice and humans are very different, then what’s the point of even trying to do research on yeast, bacteria, or flies? Who cares? Why not just work on human cells?” After all, that’s the most directly “relevant” research to medicine, and if a lot of research is funded by the NIH for the future benefits to human health, why are they funding research about yeast mating? Human cells don’t even have cell walls, and they don’t bud!

One thing I learned pretty quickly about research, however, is that there’s a lot more to those model organisms than meets the eye.

Of the past 20 or so Nobel prizes in medicine, about 14 were given for research involving model (i.e. non-human) organisms! And 8 of them were given to research on non-mammalian organisms, including yeast, nematodes, bacteria, sea urchins, viruses, and fruit flies. In that time, two Nobel prizes in chemistry were also given for research in model organisms (E. coli and yeast). The most common mammalian organisms, of course, were rat and mouse, but there were also cancer cells in there that count. So clearly, research in model organisms is somehow breaking fundamental grounds, even now!

But why?

It has to do with how easy certain organisms are to handle. Mammals obviously don’t reproduce very fast, stereotypes about rabbits notwithstanding; bacteria, on the other hand, will divide every 30 minutes when they’re happy. That’s partly why they, along with viruses of the bacteria (which grow even faster), were the basis of almost all of the revolutionary molecular biology in the 1940s and 1950s. Genetics was a whole lot easier with them because there were millions and billions of them. Biochemistry was easier, too, because you could grow gallons of them within a day or two. Yeast is easy to handle, too. A decent amount of yeast can grow overnight, and a buckets of it can be grown in a couple of days. Both yeast and bacteria are very hardy, too; you can keep them for basically forever if you stick them in some glycerol and throw them in a freezer. They’re enormously popular, even today, for basic biological research, from bioinformatics to genetics to cell biology. The awesome power of microbial genetics is a wonder to behold.

Even fruit flies, nematodes, zebrafish, and sea urchins are pretty easy to handle, compared to mice and rats. You can grow tons of nematodes and fruit flies in a few days or weeks. Zebrafish and sea urchins take longer, but they produce tons and tons of eggs (and thus, offspring) at a time.

I think in part, these model organisms have the edge because biology tends to be pretty universal, thanks to evolution. A lot of stuff discovered in yeast is relevant to humans, because though our line split off from them a long while back (maybe a billion years or so), we still share a lot of biology, from the shapes and homology of molecules to the ways our cells are organized. Similarly, insect development studies led to major discoveries in our developmental regulation, especially the hox genes. Nematode work led to the discovery of microRNAs as crucial regulators of human development and signaling. Zebrafish gives fundamental insight into vertebrate-specific mechanisms of neural development that wouldn’t be found in flies or worms. Though these animals are different from us in many ways, they have lots of similarities to us that we can find before we’ve seen them all, and we can find them fast because these organisms are easier to work with.

There are certain niches, of course, for human and mammalian research. Immunology, for example, is pretty hard to study in non-mammalian systems, just because it evolved so recently. And cancer is very hard to study in mice and rats, because their lives are so much shorter than us. Still, human cells in culture, even cancer cells, are pretty difficult to use, especially for genetics, because they don’t sexually reproduce, which makes “purebred” lines and new mutations difficult and time-consuming to come by. So work in human cells, while perhaps more “directly relevant” to human biology, is much, much harder.

Ultimately, of course, for research to contribute to understanding human biology, one needs to do experiments in human cells too, but those will get done if and when the need arises, especially by companies interested in making new drugs and cures. In the mean time, there are scientists churning away at bacteria, viruses, yeast, flies, worms, fish, sea urchins, and even sea slugs that are doing breakthrough work from which we’ll benefit years down the line.

It’s very tempting to join their ranks. It’s something I’ll be pondering for the next few months.

In my current rotation, I’ve been doing a little self-experiment; the lab has a group wiki where everyone can post things that would be relevant to everyone else, such as protocols, lab reagent lists, etc., and I figure that my lab notebook is of interest to other people. After all, it’s not just for my own records.

Thus, I’ve been keeping my lab notebook on our lab’s wiki. I know that OpenWetWare and other groups have been doing the whole “keep a lab notebook online” for a while, but I’ve been skeptical up until now about the value of an online notebook. I’m a wet lab scientist, not a dry lab scientist, and so I thought that I might run into some trouble with data and such that I wouldn’t be able to put online (or that would be too cumbersome to do so). In this day and age, though, everything is electronic. The microscope takes digital pictures, I scan in pictures of my gels, and the 96-well plate reader exports plaintext files that I can process with Python and R. Everything basically has to be able to get onto a computer anyway in order to be written into a paper.

So far, it’s been going great! It’s nice to be able to access the notebook from home or from any computer in the lab, for example, and I don’t misplace it. If I have a contact on a particular project, his contact information is always online at my fingertips. I can even search my lab notebook, or cross-reference easily! I’m a convert!

Unfortunately, I am not an open lab notebook convert, for two reasons. First, I’ve signed a non-disclosure agreement with a company to use one of their proprietary discoveries, and though we’re allowed to publish results, I figure blabbing about it all over the internet is something I’m clearly not allowed to do. Second, I work in a very competitive, fast moving, popular field, and it’s very possible that we would get scooped. We’ve already had that happen once. Even if the likelihood that someone will swoop by our lab wiki and scoop us that way is low, any little bit can be quite detrimental. And because I’m collaborating heavily, and not all of my collaborators may feel the same way about open science that I do, I am unable, alas, to endanger their own careers by putting my lab notebook on the open.

I also think that open notebooks work best in small communities, such as fields with very few people that are all friendly, or a small group of collaborators. Or even a field that moves slowly enough that it wouldn’t be possible to scoop someone based on their lab notebook. I do think that small communities make it much less likely that you’ll get scooped, as people tend not to mistreat people they’ve met and put a face to.

But in any case, as god is my witness, I’ll never keep a physical lab notebook again!

Terra Sigillata has word about an NIH open letter on cell culture line identities. Over the years, some cell lines have been shown to be contaminated by other cells (particularly by HeLa cells, those immortal, nearly indestructible cervical cancer cells popular with many cell biologists), and verifying the identity of cell lines has become a problem, many times, especially since there’s no easy cut-and-dry method to verify a cell line. The NIH is still pushing for such verification, apparently, because otherwise the research is difficult to believe.

Wikipedia has an nice list of possible cell line contaminations.

My current lab works mainly on primary fibroblasts that we isolate ourselves, so we don’t have as many problems with cell line contamination, but I’m curious as to how many other labs are affected by this.

Happy Holidays to all of you. And to those of you still in lab over the holidays, cool (and gross) seasonal Petri dish art! (h/t Miya)

One things that still astounds me is how fast the field of biology changes. If one looks back even just ten years, the human genome was yet to be sequenced (as was the genome of a vast number of organisms), and microarrays were just being invented. Lester wrote recently about how medical knowledge gets obsolete every 5 years, but individual fields in biology and medicine move much faster than that, and the pace is only growing faster.

Even in the past year, the number of things that I’ve learned that have gone out of date is pretty amazing, especially on the fundamental ways in which life works. For example, my knowledge of RNA export, the basic redundancy of duplicate ribosome genes, and the “fact” that miRNA downregulates translation, have all become obsolete, even though just last year, I took a class on the regulation of gene expression that incorporated all the latest research in the field. Actually, this isn’t the advancement of the field in the last year; it’s the advancement of biology in the last month!

I have no idea how professors manage to keep up with the changing face of biology year after year after year! Just think about all the scientists around who lived before the days of BLAST, PCR, and PubMed, to list three tools indispensable to any working molecular biologist.

The fast pace is exciting, though! Research science is like white-water rafting through through a river of knowledge; the challenge here is to keep from drowning!

I’m excited to be starting my next rotation on Monday! I just found out today that my next lab is one that studies quiescence, which is basically how cells in our body “hibernate” until they need to wake up to do something. In high school biology, you might have learned about mitosis, where cells copy DNA, separate out the chromosomes, and divide to create two new cells. Well, cells aren’t always constantly dividing, and there’s a specific “hibernation” state (called quiescence) that cells go into when they aren’t needed. Fibroblasts hibernate until you get cut, at which point they start responding to the wound by dividing and turning on genes that help with healing. I’m very excited, as I’ve never worked with mammalian cells or tissue culture before. It’ll be an experience, and hopefully really productive!

I really enjoyed my last rotation, which was in a yeast cell biology lab. I did a lot of microscopy to find out some mechanisms by which yeast cells have sex. I don’t want to get into the specifics too much, but basically no one knows how the specific mechanisms of yeast sex happens, especially how the two cells fuse together to become one cell. It was a really great project to start with this year, as it involved some very basic biological techniques, it wasn’t too hard, and I was able to start generating data right away while working on other side projects that were harder and riskier.

So overall, am I happy in graduate school? Yes, I think so. I’m learning a lot, which I always find awesome, I’m discovering new stuff, which is neat, and there’s something quite satisfying with the bench work in biology.

When I was little, I thought it was awfully boring how grown-ups would sit around and just talk. I mean, not play games, watch movies, they’d just talk! How could they spend hours doing that?

I realized today, though, that’s what I do now. I like talking to people for hours and hours. Am I grown-up now? This made me sad, and so I indulged my inner child a bit as I waited for my experiments to finish.

Dry-ice filled plastic vials that make loud bangs in people’s trash cans to startle them? Check. Water with bubbling dry ice and heavy vapors to make me feel like a mad scientist? Definitely. Squirting ethanol solution on the little crawly bugs that appear in our lab? Of course! Looking at random puddle water on a slide under the light microscope? Awesome.

Little things that keep me from growing old too quickly.

Alex Palazzo has a picture that is well familiar to anyone doing molecular biology. Alas, that is my life right now. Cloning, or rather, troubleshooting cloning, saps the spirit of all that enter biology.