The Harrowing

Well, it's official, I am now a Ph.D. candidate! It means I get to move on and continue my graduate school career. See, getting a Ph.D. is not like getting your bachelor's degree, where pretty much all you have to do is pass your classes and you get your diploma. Sometime in your second year, you have to write and present two proposals, one on your own work and where you want to go with it, and one outside your field of study. These proposals are presented to a committee of professors who are experts in the field you choose. Their job: rip your guts out and show them to you. Or at least, that's what it felt like.

Really what they're there to do is take apart your proposal and challenge you to defend it. If you handle yourself well, show that you've read a lot of background info, understand their criticisms, you get to pass, as long as there are no major problems with what you've done. Unfortunately, I had some problems. I forgot that there is a right way to ask questions in science, and a wrong way, and I did what every new scientist does and approached it the wrong way. The first thing my committee did was to point this out and re-frame my question the way it should have been asked. Then, they proceeded to point out that most of the experiments I had proposed were irrelevant to this new question. Furthermore, I had based my proposal on contradictory results from two different labs doing similar work. My committee thought it was an interesting subject, but had a quick and easy answer, one that I apparently should have seen as well.

Needless to say, I came out of this feeling pretty awful. It's never fun feeling like a stupid amateur, and it left me wondering if I even belong here in the first place. But, I don't feel that any of the criticism I received was unjustified or off the mark. It's just difficult looking at yourself through the eyes of four people who have years and years of experience and seeing all your flaws laid bare. I've felt pretty awful for the last two days, but really that's what makes it such a valuable learning experience. These are mistakes I'm not bound to make again. And I did pass the exam, on the condition that I re-write part of my proposal. Having gone through this is just going to make it that much sweeter when I finally do get that degree.

Bugs and guts: Dr. Judith Eisen explains how the nerves in the zebrafish gut affect the bacteria that live there

*Note: One of the assignments for my Science Journalism class is to keep a blog, although strangely enough it doesn't have to be an actual blog, just a word document that has all the things we would blog about. Anyway, I have't posted here in a long time (been busy), so Jen suggested I just post my assignments. Here's the first one I wrote, hopefully it's interesting enough. I'll most likely post the others as they get written.

Of all the cells in your body, only about 10% percent belong to you.

Kind of gives you a new perspective on things, doesn't it? According to Dr. Judith Eisen, a researcher at the Institute of Neuroscience at the University of Oregon, the other 90% is made up of a conglomeration of bacteria and other microorganisms. Most of these microscopic hitchhikers are beneficial to us, which is one reason our body doesn't fight them off, and many of them live in our guts. In her laboratory at the U of O, Dr. Eisen and her team study how the nervous system another vertebrate––the tiny zebrafish––affect the population of microbes that live there.

Normally we envision bacteria and other "germs" as being detrimental to our well being, so it seems odd to think that innervation in the gut affects the microbes, and not the other way around. But this is exactly what researchers in Dr. Eisen's lab have found. During a genetic screen, a process by which animals with interesting defects are generated by randomly mutating their DNA, members of her lab found a zebrafish mutant that lacked pigment cells. Upon closer inspection, they found that it also lacked nerve cells in its intestine. The lack of nerves causes the muscles in the intestines to fire randomly, or not at all; this is in contrast to normal intestinal muscle, which have controlled rhythmic movements.

Examination of the microbes living in the gut of these mutant fish revealed that there were many types not found in normal fish. Eisen’s team hypothesized that the movement of the intestinal muscles helps move the microbes into their proper position. In order to test this, they set up a simple experiment using two different types of bacterial "food". The movement of the food through the intestine can easily be monitored, thanks to the fact that zebrafish are transparent. Normal “wild” zebrafish were initially fed green bacteria, and its movement was monitored over a stretch of several days. Then, the fish were switched to red food. Over time, it was possible to see the green food disappear, replaced by the red food. In the mutant fish, however, all of the food was trapped at the entrance to the intestine. This data helped prove that their hypothesis was correct.

The reason Dr. Eisen's lab has chosen this area of research is that it is directly applicable to human health. One disease in particular, Hirschsprung's disease, is caused by a lack of nerve cells in the intestine. The mutant zebrafish studied in her lab is a good model system in which we can study and understand this deadly affliction. Furthermore, Dr. Eisen stated in her presentation that many neurological diseases have a related gastrointestinal (GI) component. At this time, it is difficult to determine if the GI problems cause the disease, or the other way around. Hopefully, the work done by researchers like Dr. Eisen will help to clear up this conundrum.

Learning to Walk

So, normally I'm against New Year's resolutions. I've always thought that if there's something in your life you want to change, then change it. Why wait for a holiday that really has no significance to decide to start being a better person (whatever that means)? But I've recently decided to make a change in my life, and my decision just happens to coincide with New Year, so I guess I really do have a New Year's resolution this time around. I've decided that I need to learn how to walk.

Now obviously I can walk, in a literal sense; I mean it metaphorically. I've been blessed with the ability to learn things quickly, which allows me to become pretty good at most things without too much effort. I'm not claiming to be a master at everything, and there are some things that I'm just plain bad at, but for the most part I can perform at an above-average level at most tasks. Because of this, I've gotten in the habit of trying to do too much too soon. For example, not too long ago I had my first meeting with my advisory committee, the purpose of which was to explain to them what work I'm currently doing and where I'll be going in the future. One of the techniques we use is sort of specific to worms, so I knew I needed to go into a little more detail when describing it. I made this really complex powerpoint slide with tons of animation for my talk, and it looked great. I was (and am) proud of it. But I got over-confident. I was thinking "Okay, I've got this really good slide to explain the most complicated part of my talk, and all the rest of this is just stuff I do everyday, so it should be easy!" I didn't even practice my talk before I gave it; hell, I didn't even finish it until an hour or so beforehand. But because I had done so well on that one part of it, I was convinced it was going to be a home run.

It wasn't.

In fact, I kind of made an ass of myself in front of my committee. Afterward I felt pretty humiliated, not because my talk didn't go well, but because I know I'm capable of more, and I just didn't even try. And I've found myself doing it again. I've always had an interest in martial arts. I've read several books on various types of martial arts, I'm familiar with the various strategies and philosophies of many different styles. When I watch a UFC match, I try and relate what I've read to what I'm seeing, and try to figure out what I would do in different situations. But I've never actually had much hands-on experience with martial arts. I just recently joined an MMA gym to try and change this, and once again I'm trying to run before I can walk. Instead of taking my time and really getting the most out of each drill, I'm busy trying to just "be good" at everything by relying on my conceptual knowledge. But it doesn't work, and I can tell you from experience, getting punched in the face is a really good, quick reminder of that.

So that is my new goal: learning to walk. I'm going to learn to take my time and really focus on building a good foundation before I move on to more challenging and difficult tasks. Unfortunately the problem with learning is that you have to screw up a few times before you can get it right, and I really don't like making mistakes (especially when they result in pain). But what's life without a few bumps and bruises?

It's a full life, and a pleasant one.

Update time! Quite a lot has happened since I last posted. First and foremost, I have officially joined a lab! It's the same lab I was in Fall quarter, meaning that I'm back working on worms. I am definitely happy to be here. It's nice to finally feel like I've got a home. I have my own bench space, my own desk. I even got a new computer(which I am using to write this blog post). It's a mac, which I'm not too thrilled about, but (a) if I had complained enough, I could've gotten a PC, (b) it's free, so I'm not going to complain, therefore (c) I've got a new mac. It's actually pretty sweet, and CERTAINLY better than what I had before. I also really like the people in this lab. I kinda forgot how much I liked it here first quarter, but now that I'm back, I totally remember.

The work itself is a little tedious and boring, but it definitely keeps me busy. We're currently in the middle of a genetic screen; for those of you not familiar with genetics, it basically means we're looking for new stuff. The way this works is that we use chemicals to induce mutations in the DNA of "teenage" worms, then let them reproduce. The babies will have defects, which is what we want. The difficult part is finding ones that are interesting; in this case, we're looking for mutations that cause defects when the worms are grown at a higher temperature, but don't have the same effect at lower temperatures. These are really rare. Not only that, but a lot of the ones we find are ones we already know about and aren't interested in. So pretty much this next year for me will be devoted to sifting through a haystack looking for needles.

One other perk of joining this lab was that I got to go to an international conference in Germany a few weeks ago. I'll do a separate blog post about it, but for now I'll just say that it was a really awesome trip.

So yeah, all in all, things are looking up for me. I am super glad it's summer time. I've got a lot more free time on my hands now; I might even start writing more (doubtful). Okay, break time's over... back to the worms!

Death by Powerpoint!

     So I just read an article in the New York Times talking about the over-use of Powerpoint in the military and how it's becoming more of a hindrance than a help. I have to say I agree with them. I see several powerpoint presentations a week, and honestly it's hard to pay attention, or sometimes just to stay awake. Powerpoint is really good for showing pictures or movies, but too often people try to use bullet points to actually convey their information, and usually one of two things happens: (1) they summarize way too much, or (2) they write full paragraphs for each bullet.
     In the first scenario, the presentation becomes useless if you're not actually there to see it. Most of the classes I've taken after high school have used powerpoint extensively, and often teachers will post their presentations after class. Some students try to use these as an alternative to showing up, which obviously doesn't work out well. But even if you show up, and miss a talking point, you can't rely on the presentation to give you the information you need. Now personally I don't think anyone's going to leave with 100% of the information presented every time, whether you're using powerpoint or not, so really it comes down to your ability to sift out the crap and write down what matters, a skill not easily learned. But the problem (at least, in our military it seems) is that some people are trying to use powerpoint presentations as little more than illustrated memos, which seems (obviously) destined to fail.
     If you used powerpoint as described in point (2), you might be able to get away with it. But if you're going to do that, you may as well just write a word document and attach some pictures, which would be much easier and probably more effective. Not only that, but these type 2 presentations are terrible! Usually these are the kind made by people who can't bother to memorize what they're going to say, or simply don't know the subject matter that well. The presentations then are reduced to simply reading the slides aloud in front of a group of people. And if they do actually have a speech written, then your audience ends up trying to read all the text and not listening to what you have to say. More often than not the text is tiny, so people are squinting and having to work harder to read it, further obliterating any attention being paid to the speaker. It sucks.
     The problem here is of course not Powerpoint, but the way people use it. The program itself is pretty awesome if you take the time to learn what features are available. But one thing that was interesting about the article is that throughout the whole thing they have quotes from military personnel demonizing Powerpoint, but then at the end include one sentence saying "No one is suggesting that PowerPoint is to blame for mistakes in the current wars, but..." It seems the problem is the people, not the program. Only a poor craftsman blames his tools. There is one quote, though, that I thought was very appropriate:

"Senior officers say the program does come in handy when the goal is not imparting information, as in briefings for reporters."

It seems pretty pictures help when you're trying to say nothing.

Reporting Live from the Surface of the Moon!

Hey everyone! I am officially back in the blogosphere; I'm sure I've been terribly missed. It's not that I haven't had anything to write about, I simply haven't had the time or the energy. But things are looking up (for now), and so I've decided to start writing again.

So far, this quarter has started off great. I'm in a new lab, doing new work, and I really like what I'm doing. This quarter I've joined a genetics lab, using the model organism Drosophila melanogaster. In English, fruit flies:

This particular lab is focused on neuron development, and we study neurons in fly eyes. It's actually pretty sweet. There's all kinds of little molecular genetic tricks that we can use that allow us to create individual mutant cells surrounded by normal cells. This way, we can directly compare the neurons from the same animal (which is an important consideration in genetics). It also means that we can now look at what effects certain mutations have in just the eye cells, instead of in every cell. This is important because a lot of mutations are lethal, and it's hard to study how an animal develops if it's dead. What this means for me is that I get to spend a bunch of time collecting virgin flies and dissecting brains. And when the whole fly is less than 2 millimeters long, it's nearly impossible to do.




These guys make it look easy, but trust me, it's actually pretty tough. However, I did manage to pull out one intact brain in my morning dissection practice, so hopefully I'll be able to work up to this level of proficiency.

The other thing that's awesome about this quarter (aside from the fact that last quarter is over) is that I'm not taking a class. So really, the only thing I have to do is work and go home. It's making things so much better. Trying to do research work, teach a class, and take a class, on top of all the various other things that pop up during the week, is just a recipe for disaster. It's not the fact that there's so much work to do, it's that everything becomes just another thing on the list. The mentality switches from trying to focus and learn something to just getting everything done. And even though everything did get done, it wasn't done nearly as well as it could have been, so then I feel like I've done bad work, even if I haven't. So yeah, this quarter I'm just doing my fly work, and teaching a class. I'm super stoked.

My First Tattoo!

I finally did it! I got my first tattoo done today. Actually, it's just the line work, I still need to get it shaded in. I think it's going to look really good when it's all finished. It took just under two hours to get it all done. It really only hurt in a couple of spots, near my lats and my lower back, but even then it wasn't painful. Kinda feels like a sunburn now. So yeah, I'm pretty excited about it, but I can't wait until it's completely finished. Hooray!


Update: I've been getting a lot of questions about why I got this particular tattoo. I actually posted about it a while ago, but because of the way Blogger is set up, it's all the way back in October(or some other month). So here is a link to that previous post explaining everything.

The Climate Change Controversy...thing...

     I'm refusing to call it "Climategate." Every time some new government conspiracy (which are never really as bas as they're made out to be) comes to light, the media grabs ahold of it, blows it way out of proportion, and adds "-gate" to the end of it. It's like a new suffix in our language, and it's completely fucking ridiculous. The only one that deserves to end in "-gate" is Watergate, and that's only because that was the name of the place where it happened (okay, that's a simplification, but you get the point). Once again our eagerness to slap easy-to-digest labels on everything rears its ugly head. Ughh!

     Anyway...On to what I really wanted to say on the subject. I was originally going to call this post "Bittersweet Vindication," but then I realized that it was a bit too early to call it vindication. You see, I've never really been too concerned when it comes to the environment. I don't recycle, I don't know how big my "carbon footprint is" (and don't care), and I'm not frightened that the world will be uninhabitable for my children (because it will be fine). I've long considered all the hype surrounding global warming to be a product of simple hysteria and people's desire to do good. So when the news came out about those "hacked" e-mails from climate change scientists pulling mathmatical tricks and hiding declines, I felt pretty good about myself for not giving in to paranoia.

     But, part of being a skeptic is basing your opinions on facts and reason, and this seemed simply too good to be true. I may not believe in global warming, but I don't think it's all a government conspiracy either. What would they possibly stand to gain from having us believe it? Countries around the globe have spent billions of dollars trying to reduce carbon emissions, yet few of them have actually hit their goals, and if the alarmists are to be believed, it hasn't made any difference! Individual politicians have benefitted from our belief by saying that they'll do something about it, but they're simply using this issue like they would any other hot-button issue. There are plenty of others to exploit without needing to drum up fear about global warming. On top of all this, it's actually fucking up our daily lives. There are counsellors out there who specialize in treating "green guilt." Some people feel so badly about global warming that they have given themselves a psychological condition. One of the professors at my school said that he doesn't drive because he "feels bad about spending the carbon." I think this has gotten way out of hand.

     Turns out those e-mails weren't "hacked," they were "leaked," and there's a difference. They were being compiled for a freedom of information act document, to be released to the public. These were going to come out anyway; the only bit of foul-play is that someone released them early, no doubt to coincide with the Copenhagen conference. Now, I will admit the language in them is fairly suggestive (I'll also admit that I haven't read them, only what I've seen on internet videos both for and against the conspiracy idea). When you're telling someone else to delete their e-mails because of sensitive material, that sorta shows that you're trying to hide something. Maybe they are hiding something, but I would be more inclined to believe that they're trying to hide their ignorance on climate change as opposed to it all being made up. I think what happened is that someone raised a red flag, the world panicked, and these guys got so caught up in their newfound positions of respect and authority that they didn't want to say "It's actually not that bad." Again, I have no evidence for this, but I think it's much more likely than any of the other scenarios I've heard.

     What's so bittersweet about this you may ask? It seems to me and many of my new colleagues that the public in general doesn't trust scientists. I don't know exactly why this is, but I have an idea. I think it's because we go into our labs, all secretive and hidden away, and come out with data that's either incomprehensible to the general public, or that contradicts common sense. I want to clarify that bit about it being incomprehensible. I'm not saying that they are incapable of understanding, I'm saying they don't have the background knowledge/vocabulary necessary to make sense of the data. But I think a lot of people see it the other way, that they're too stupid to make sense of it, so they don't even try. I also think that when it contradicts what they've been previously told, they're unwilling to try to understand. So here we are, trying to expand the depths of human knowledge, to further educate everyone, and many people just aren't willing to listen. This is the position we were already in. Now these e-mails come out, and the media/conspiracy theorists/global-warming deniers start screaming about how it's all a lie. You can imagine what sort of effect this has had on the image of scientists in the public eye. Who's going to listen to us now? It's a sorry state of affairs.

     So there it is, my opinion on this whole controversy. Honestly, I don't think it'll have much of an effect outside of further polarizing both sides. The crazies will simply be crazier, on both sides of the issue. Those who can make money off this situation will. And in the end we'll still be spinning our wheels arguing about who's right instead of doing something useful. Such is the human condition.

What I Do All Day

I heard that a few of you are disappointed that I don't talk about myself a little more often, so I figure I'll write a little post about how I'm doing and what my schoolwork is like. The short answer is that I'm doing great. I love being in school. I love it. I feel like this is what I was made for. At first I was really worried about coming back after being out of the game for three years; not just out of school, but not having even thought about science for those years. So I was relieved (and more than a little surprised) when everything came right back to me, as though I'd never left.
They definitely keep me busy around here. I'm only taking one class, but believe me, it's enough. Luckily for me, though, it's a really interesting class. Not only that, but after each lecture I feel like I'm just a little bit closer to the cutting edge of my field. It's a weird feeling. You go to school for years and years, and it seems like there's always more to learn, and now I'm getting to the point where people ask questions and the answer is, "We don't know yet." It's exciting to think that I'll be helping to push the boundaries of human knowledge.
On top of my class, I've been teaching a general chemistry lab class. It's similar to the TA work I did at Eastern, so I'm not too out of my element, but it's definitely more labor intensive. Aside from doing all the grading, I have to actually keep a grade book, prepare short (really short) lectures, and even discipline the class if necessary (I've only had to do this once, thankfully). I'm like a real teacher now; some of them even call me Mr. Lowry, although I try and get them to call me Josh. There is still a bit of a difference, though; I doubt too many high school teachers have students asking for their phone numbers.
And of course there's my research, which is the really exciting part. In fact, I can't wait until I no longer have to take classes so I can spend my time doing my research. I've been working on a few different projects since I showed up this summer, and one of them has yielded some exciting results. What we do is something called RNAi, where we feed our worms this special food that targets one of their genes and shuts it off. Then, we look at one-celled embryos, watch them divide, and see if there's any difference between our mutant and a normal cell. Most of the time there's no difference; I mean, worms have ~30,000 genes, and we're shutting off one. But every once in a while, you get something exciting, and that's what happened to me. Here are some videos I made of this first cell division:



In this one, the DNA and the centrosomes (no, I don't expect you to know what they are) are labeled with a special protein that glows green when you shine a laser on it.


This one shows microtubles labeled in red. These both show the same mutant, just with different cell parts visible. I know they're not in color, but when I look at them under the microscope those are the colors I see. When we process them, they lose their color. Still, it's pretty cool to be able to watch all this happening right in front of you. The first cell division actually takes between 10-15mins, so this is time-lapse video you're watching, but still, this is an actual cell going through an actual division. I think it's cool every time I watch it.

So yeah, that's what I've been doing. It keeps me busy, but I'm loving every minute. And with that, it's back to work for me.

I Just About Pissed Myself...

...because I was laughing so damn hard at this!

Apparently, it's not enough to try and guilt kids into not having sex, to lie to them about the evils of birth control, and to tell them masturbation leads to blindness. Now, kids aren't even supposed to give each other proper hugs. That's right, the "front hug" is now officially sinful. What used to be a simple, innocent gesture of friendship and closeness is now sexually charged and awkward. But don't worry, there's an alternative way to show how much you care, the Christian Side Hug! That's the actual name; I did not add the word Christian to this. You want proof? Here's a little video spelling out the dangers of front hugs (and kissing, but we already knew that was wrong), presented in such a way as to mesh with pop-culture attitudes, so that kids will pay attention.

Speaking of paying attention, keep an ear out for the sounds of sirens, gunshots, and threats of violence in this song. Just like in the Bible, violence is okay, but sex is evil.




I have a feeling this is just the beginning. Pretty soon it'll be the Christian Handshake (not to be confused with the Freemason Handshake, or the Cool Black Guy Handshake), then the Christian Wave From Across the Room, and ending with the Christian Separate Bedroom (for married couples only!). It's an exciting time to be a Christian!