Posted by: unlikelygrad | June 19, 2015

paperwork and preparation

I have spent the last couple of weeks jumping through the bureaucratic hurdles to get my status at MyU switched from student to faculty. This must not be a common process because I’ve gotten a lot of misinformation from various flunkies.

For example, one told me that I needed to redo all of my paperwork, including the direct deposit form, and there would be a “trial run” for the first paycheck, which would mean picking up an actual paper check on payday (even though my paychecks have been direct deposited into the same savings account for the last ~5 years). I couldn’t find a deposit slip for my savings account, so I filled the form out with my checking account info instead. Later, the person in charge of bank transfers called me to ask whether I really wanted the money going to my checking account, or whether I’d just like to keep it going to the savings account that was already on file. Obviously I didn’t need to futz around with the direct deposit paperwork in the first place.

I was also told by the computer help desk guy that I absolutely could NOT keep my student email–I’d be assigned a different email for use as a faculty member, since I would need different permissions. And since I can’t have two email addresses assigned to me, my student email would disappear fairly quickly. ACK!! Right now I have almost everything going to that address; I had planned to change things over to a gmail account over the course of the summer, but hadn’t gotten around to that yet. Immediately I ran home and started notifying all sorts of people of the new address; I also frantically tried to figure out how to download the messages using Apple Mail (since I’ve always only used the web mail feature). A couple of days later I went back and was brought upstairs to the system administrator…who told me that I would just keep my old email address. Grrrr!!

All of this paperwork has interfered with my prep time for class. Since this is an accelerated class (one semester’s worth of material in 6 weeks) I’m not going to have much time to do lecture prep once it starts. So I’m not only trying to put together the usual start of term documents–syllabus, lab schedule, etc.–but also trying to get as much lecture prep done as possible before the first week hits.

It all starts Monday. It’s going to be an adventure!

Posted by: unlikelygrad | May 24, 2015

what’s next?

Honestly, I don’t know.

I have a summer job–adjuncting at MyU–but I have no job lined up after that.

I want to teach, of course, but at this point I will do whatever it takes to support my family.

I’ve applied for ~45 jobs so far (academic & industry) and nothing has panned out. Don’t get me wrong; I’ve had phone interviews and even, in one case 3 successive interviews, but I only end up with rejections.

It’s depressing.

Posted by: unlikelygrad | May 24, 2015

the secret

As anyone who’s in grad school has learned, the first part of a dissertation defense is open to the public; the part in which the committee questions the candidate is private. I always found this frustrating because, if I didn’t know what was coming, how could I prepare for it?

The closer I got to my defense, the more worried I got. I had an officemate who was in with his committee for close to two and a half hours (after the public part!). Granted, this is a bit extreme, but how did I know that I wouldn’t end up in that situation? (Dr. Green was particularly hard on me when I took my oral exams–he questioned me for over an hour and would have kept on going if the other committee members hadn’t demanded some time for questions, too.)

Needless to say, I was surprised when my committee wrapped up the questioning in a bit under an hour. My thought as they ushered me out for deliberations was, Is that all? Not only was the questioning short, it was relatively easy. The questions were thought-provoking but I was able to answer them without too much effort. I even cracked a few (topic-appropriate) jokes.

That evening, at a party Dr. Hand-Waver gave in my honor, I was talking with Dr. Sharp (not on my committee) and mentioned that I found the defense amazingly easy.

“In what way?” she asked.

“Well,” I replied, “It didn’t feel like an interrogation to me, the way that my other committee meetings did. It felt more like sitting down and having a conversation with friends.”

She smiled at me. “Well, that’s what we look for, isn’t it? Once you pass, you become a colleague. We want to see that you can talk to us as a colleague. It’s amazing how few students get that.”

So there you go. That’s what you’re shooting for as a grad student.

Posted by: unlikelygrad | May 22, 2015

Doctor Unlikely!!!

If I have fallen off the writing wagon the last six months, I apologize deeply.

Things have been crazy here: dealing with (a couple of fairly serious) issues with the children, job hunting, and–of course–finishing up the dissertation.

Yesterday I defended my dissertation. (There will be another, longer, post on this later.) After the committee deliberated, my advisor came out to fetch me and congratulate me. As I re-entered the room, various committee members shook my hand and said congratulations, and then, finally, Dr. Green–who’d been sitting in back–said, “Congratulations, Doctor!”

And that’s when it started to hit me. I did it!! Almost 24 hours later, I’m still a bit disbelieving that it’s (mostly) over; the euphoria hasn’t hit yet.

Posted by: unlikelygrad | November 15, 2014

I should knit…

I’ve always wanted to learn to knit, particularly because I have trouble sitting still unless I’m doing something with my hands. I’ve tried learning but have yet to get the hang of knitting.

A couple of days ago I got a fresh batch of bacterial strains from our collaborator. They arrived in Petri dishes on agar:

IMG_1947

My job was to transfer them to growth media so I could make freezer stocks for use in experiments. That sort of work is best done in the culture lab, which is unfortunately in a different building than my lab. So I had to bring the agar plates outside.

Unfortunately, the high temperature that day was around 10 F. I really didn’t think going outside in that cold would make my bacteria particularly happy, so I looked around for something I could use to insulate them. I found an old sweater of my son’s stuffed into one of my desk drawers and decided that would work perfectly.

I’ve since used the “bacteria sweater” (as I’m now calling it) for insulating my cultures on several runs to/from the culture lab. I’m starting to think it would be a good idea to have insulating sleeves for things like Petri dishes, Falcon tubes, and such. I wish I could knit some, but since I can’t, maybe my son Will could do it…

Posted by: unlikelygrad | October 31, 2014

Why doing outreach is good–from a selfish point of view

Most people I know in our department do outreach because they have to.  You know, they (or their PI) put some blurb about it in the grant proposal, and now they have to follow through.  Accordingly, I’ve heard it said that you should do the minimum amount of outreach that you can get away with.

Baloney, I say.

* * *

I discovered long ago that if I am sitting, staring at a manuscript and trying to force words on the page, I get stuck easily.  Back in California, I found instances of writers’ block to be the perfect time to go outside and deadhead my roses (which bloomed year round).  Here in Colorado, I try to write at home so I can work on home improvement projects (painting, etc.) at those times.  I also get my brain unstuck by washing dishes, folding laundry, and such.

The reason this works is that sometimes you have to back away from a problem and let your subconscious work before you can get past your roadblock.  Doing mundane tasks allows you to move your primary focus away from the important work but also leaves enough brain power to keep the thought process simmering on the back burner.

For me, doing outreach serves roughly the same purpose as these mundane tasks.  Except it’s better in some ways, because my brain is still in science-thinking-mode.

* * *

I think one of the pervasive problems in science today is that people are getting hyper-focused on their areas of specialty.  Don’t get me wrong; I believe that people have to specialize to a large degree.  But I also think the big breakthroughs come when someone is able to step back, look at the bigger picture, and bring something new into the field that other hyper-specialized people don’t even think about.

This is another bonus about outreach: if you’re doing it right, you’re addressing broad topics that wouldn’t normally come up in your research.  And sometimes, as you learn more about these topics that are only vaguely related to what you’re currently studying, you come up with new research ideas.

* * *

The last self-serving reason for doing outreach is that it makes you feel cool. When you’re working with middle-school kids, you never feel like you have impostor syndrome. (The same does not hold true for me in academia!)

A local middle school is developing an experiment that will go up to the ISS in spring (assuming that the Antares disaster doesn’t mess up the schedule).  They asked a club I’m part of for help.  I went along because, hey, outreach.  And space.

They ended up being very happy to see me because there’s no real biology department on campus and I’m the closest thing you can find at MyU to a biologist–I know about agar, and nutrients, and designing experiments with living creatures, and things like that.

I love this project because it’s so much simpler than the stuff I do for school.  Don’t get me wrong–it still has lots of complexities, and the kids are going to be hard pressed to get all of the variables sorted out before launch.  But compared to what I do, it’s a piece of cake.  I can take in the information they give me, figure out what the concerns will be, come up with solutions, and help them figure out how to test which solutions will work best. At times when I’m struggling to see myself as a decent scientist, it’s nice to prove that my research skills are actually decent.

* * *

Bonus reason: the laughs.  The other day we were brainstorming how to test performance in microgravity.  I explained the science behind the “Vomit Comet,” trying to steer them towards the idea of dropping the stuff from heights.

One of the kids came up with a better solution.  “Let’s take it with us on The Tower of Doom at Elitch’s,” she suggested. Bwahahaha. Yeah, that would probably work.

Posted by: unlikelygrad | October 23, 2014

Don’t be too quick to judge

This post is written as a response to an article I saw on social media yesterday. A friend (not a scientist) linked to the following: the top 7 wackiest examples of government spending.

Of course, everything in the article is made out to sound ludicrous. And maybe some of them are. But while I may disagree with some of their choices, an article like this is simplified to the point where you cannot understand the justification behind any of the studies. So let me explain what I see as the reasoning behind #2, “watching grass grow.”

The Department of Interior spent $10,000 to monitor the growth rate of saltmarsh grass. In other words, the government is paying people to watch grass grow. On the bright side, they have not started paying people to watch paint dry.

First of all, $10,000 is peanuts (I’ll explain why in a moment).

Second of all, speaking as a scientist who’s done environmental work, I’m guessing that this involves weekly or monthly visits to measure the grass–they aren’t actually sitting there watching the grass.

Finally, why would the Department of the Interior care about the growth rate of saltmarsh grass? Because one of the best ways to prevent damage from hurricanes etc. is through the restoration of coastal wetlands, and the more you learn about how these wetlands grow, the more effectively you can restore them. If, by spending $10,000, they save a million dollars in damage (which, considering the amount FEMA pays out for storm damage over the course of a decade, is quite a modest sum) it is a worthy investment.

* * *

So, on to the money issue. I said that $10,000 is not very much money. Why? First of all, many institutions take 50% of a scientist’s grant money to cover overhead costs–upkeep on the lab space, paying for electricity, and so on. So our poor PI (that’s “principal investigator,” the chief scientist in charge of the project) is left with $5,000 to run the study.

This amount has to cover supplies, travel costs (say, 20 miles round trip every week to the study site over 2 years), and pay for the scientist doing the monitoring. The monitoring scientist, who is probably not the PI, could very well be a grad student like me. My salary + benefits (health insurance, tuition) runs roughly $36,000/year. Suddenly, $5000 doesn’t sound like so much, right? Even 1/5 of that (for a project that runs one year) is a bit over $7000–$5000 doesn’t even begin to cover it!

Every grant submitted to the NSF and EPA (not sure about other agencies) require justification. The proposal must address the proposed benefits to society. It is not enough to want to do science or to come up with something interesting or “cool-sounding.” It has to benefit society in some small way. (Many agencies also require an outreach component, which means that part of the money is being spent on public education.)

* * *

The article concludes by saying:

While some of these waste examples seem like a drop in the bucket, cutting wasteful spending is important to build momentum to tackle even more difficult and pressing issues, like entitlement spending.

Moreover, the national debt is currently $17.9 trillion–and growing. Waste reform is just one of many steps needed in order to bring down the national debt, and ensure a prosperous future for the next generation.

Well, let’s think about this for a moment. Let’s say a person was deeply in debt. Let’s say this person lives in a McMansion with a monthly payment of $5,000 per month and leases a luxury car for $500 per month. Let’s say that this person also stops by Starbucks twice a week to pick up a coffee. Should this person start by cutting out their cappuccino? Wouldn’t it better to say, “Hey, you can get a decent car for half that amount per month” or “If you downsize your house, you could save a couple thousand per month?”

The federal budget for 2014 includes $1.235 trillion in spending. (All figures in this section are from Wikipedia.) Of that, two agencies that exclusively support science–NASA and the NSF–receive about $25 billion, or about 2%, while three that might contribute a modest to reasonable amount of their budget to science–the Department of the Interior, the EPA, and the Department of Energy–are allotted $48.3 billion, or about 4%.

By contrast, the Department of Education receives $71.2 billion–almost as much as the first five agencies mentioned put together. (Constitutionally speaking, I’m pretty sure education is supposed to be governed by the states, not the feds, but that’s neither here nor there.) The National Intelligence Program gets $48.2 billion. And the Department of Defense gets $526.6 billion.

* * *

Don’t get me wrong. I believe in having a strong military. But if we cut 20% from the defense budget, we’d still have a pretty strong military. If we put half of that back into the science budget, we could understand so much more about our earth and create science jobs. We barely understand the dynamics of the ocean, and yet we only have 24 research vessels in our fleet (6 of which aren’t big enough to go into the deep ocean). Meanwhile, the navy has 430 ships…

I think we have our priorities wrong. Defense is all well and good, but money for science can potentially improve people’s lives…and money for collaborative science, with shared projects between nations, can build bridges and promote peace in ways that military action never could.

Posted by: unlikelygrad | October 7, 2014

What hydrogen peroxide does to your body

I cringe every time a friend of mine posts an article like “25 uses for hydrogen peroxide” on Facebook.  Usually these are the same friends who rant about the evils of ethylparaben, propylene glycol, or the like.  Well, I’ve spent the last 5 years learning what cells do with hydrogen peroxide…and what it does to cells.

Executive summary: Honestly, people, hydrogen peroxide is much worse news than propylene glycol.  I would not brush with it, gargle with it, or even put it on cuts.  Yes, it kills germs.  But why? Because it can do serious damage to ANY cell.  Including yours.

* * *

Now here is the science behind my statement. Your cells always have a small amount of hydrogen peroxide in them, for two reasons. The first is that cells actually use hydrogen peroxide to “digest” fats into smaller particles.  They do this because… drumroll… hydrogen peroxide is good at breaking down fats.  Did you know that your cell membranes are also made of fats?  Yes, in high concentration hydrogen peroxide will break your cell membranes.  It does that to germs, too, which is why it is such a good disinfectant.  Obviously, your cells don’t want to kill themselves, so they use hydrogen peroxide in a very specialized part of the cell (an organelle known as a peroxisome) so it can’t impact the rest of the cell.  And all around the peroxisome, there are specialized enzymes–catalase and peroxidase–designed to break down hydrogen peroxide and keep it from getting out to the rest of the cell.

The second reason that cells have hydrogen peroxide revolves around what we chemists call ‘the four electron reduction of oxygen to water’–what biologists call respiration.  As oxygen is reduced (gains electrons) it passes through four intermediates known collectively as reactive oxygen species (ROS).  These intermediates are known as superoxide radical, hydrogen peroxide, and hydroxyl radical. (For plants, the reverse reaction, photosynthesis, is even more strongly implicated in ROS production.  Having done a lot of work with photosynthetic critters, I understand the photosynthetic ROS production pathways  a lot better than I do than those linked to respiration.)

Normally there are enough electrons around that the reaction goes all the way to water, but there are enough “leaks” in the system that (usually) superoxide can get out of the pipeline and into the cell.  This is why there are plenty of enzymes around the mitochondria and chloroplasts–superoxide dismutase to break down superoxide (and turn it into hydrogen peroxide) and catalase and peroxidase to break down the hydrogen peroxide.  The damage is contained.

It should be noted that of the three ROS produced by respiration, superoxide is highly reactive and can do lots of damage; hydrogen peroxide is the least reactive; and hydroxyl radical is the most reactive and toxic.  Superoxide and hydroxyl radical, especially the latter, are the most common “free radicals” implicated in cancer, as both can irreparably damage DNA.

So what about hydrogen peroxide?  Well, even though hydrogen peroxide is less reactive than the other two ROS, (1) it is still capable of doing damage; and (2) if it meets up with any metals (and you can find those in the cell in small concentrations, as they serve as the basis for many enzymes) it will react to form the highly reactive and damaging hydroxyl radical.  That’s why the cell is so intent on keeping hydrogen peroxide low–not just because it can do damage itself, but also because it can turn into a highly toxic radical species.

* * *

Let’s go back to the uses for hydrogen peroxide you frequently see proposed on the net, like using it as a mouthwash. There are several problems with this. First of all, hydrogen peroxide can diffuse through the cell membrane.  If you were to gargle with a reasonably concentrated solution of superoxide, it would damage every cell membrane it came in contact with, but that’s it.  Superoxide is a charged species and therefore doesn’t go through the cell membranes very well.  But hydrogen peroxide, which is both electrically neutral and similar in size to water can easily pass through the aquaporins designed to let water through the cell membrane.  So it gets inside your cells.

But so what?  Aren’t there enzymes designed to break it down?  Well, yes there are, both inside and outside the cell. However, kinetics must be taken into account.  CONCENTRATION MATTERS. The more hydrogen peroxide there is, the longer it will take for the enzymes to break it down.  The hydrogen peroxide in  your cells is usually present in nanomolar concentrations; the hydrogen peroxide you buy at the drugstore is just a bit under 1M in concentration.  So you are hitting your cells with roughly one billion times the amount of hydrogen peroxide they’re used to dealing with!

* * *

In short–hydrogen peroxide can damage your cells in the same way it can damage germs.  I would not use it topically and I particularly would not consume it in any fashion. It’s ok to use it for a disinfectant on non-living items, but be sure to rinse well with purified water to get rid of any residues. (There’s a reason hospitals use alcohol as a disinfectant instead of peroxide–it evaporates quickly, leaving no residue behind.)

 

* * *
Edited to add: I have been asked for my sources.  The most comprehensive source for this sort of material is “Free Radicals in Biology and Medicine” by Halliwell and Gutteridge.  I think they’re on 4th edition now?  It’s a textbook, but it is far more understandable to ordinary folks than scientific papers.  It’s become my Biology Bible for writing my dissertation.

At some point this will be revised to be even more scientific and will include many more sources, but I’m not likely to get around to that until I’m writing my dissertation intro, which will cover a lot of hydrogen peroxide cellular biology (among other things).

 

Posted by: unlikelygrad | August 31, 2014

The last year of grad school…

…is kicking my butt.

We’re down to roughly the last 6 months here (last 4 months if all goes well) and I’m working like a maniac.  Luckily, lots of it is writing, which I can do at home or in waiting rooms during my kids’ appointments, etc.  Unluckily, not all of it is writing–the bacteria project is going full steam ahead, which entails occasional overnights in my office so I can monitor stuff every couple of hours for 24 straight hours.  I hope to have all of the lab work done by the end of October.

Despite working way too much, I somehow have time to keep an eye on the job market.  My resume and CV are updated, so hopefully I can take either the academic or industry route.  I would prefer academia, of course, but my primary goal is to be able to support my kids financially. (Read: industry is better than adjuncting.)

The stress is taking its toll on me.  My immune system is weak, so I get sick often; and my vision is going downhill at an alarming rate.  (Just went to the eye doctor and left with a prescription for…gulp…bifocals.)  I have to finish before it kills me.  Literally.

Posted by: unlikelygrad | August 15, 2014

why I post about depression

I first experienced depression during puberty, maybe age 13 or so.  It made me unhappy at first; by age 14 I was downright miserable, and by 15 I was suicidal.  Not once did I ever think of getting help.  Why not?  Because, obviously, if I was suicidal, there was something wrong with me.  I mean, really, only the hopeless cases get suicidal!

At age 16 1/2 I left for college, still quite depressed.  At the highly competitive and very stressful university I attended at first, I failed classes.  This did not help.

After I dropped out of that school and got married (age 18), I spent a semester in community college, trying to raise my GPA enough that I could apply to another university.  While I was waiting in line to register for classes–it was a long line, and it moved very slowly–I picked up a school newsletter to read.  One article was about how to know if you had depression.  I looked down at the list of symptoms–they almost all applied–and almost started crying, because suddenly I knew.  I was not horribly bad: I was sick.

I wish I could say that I got help right away, but I didn’t.  When I went home and told UnlikelyDad, he quickly shut me down: “Nonsense.  Everyone gets blue now and then.”  And so I didn’t do anything about it.  But I knew, and knowledge is a powerful weapon.  Over the years I learned things that helped me manage the depression–a healthy diet, exercise, etc.  After my second bout with suicidal thoughts, I went to the library and got a book on Cognitive Behavioral Therapy, which was very helpful.  (By this point, UnlikelyDad was no longer openly against therapy–but he refused to let me have the money to go to therapy, which our insurance didn’t cover, or use of the car to go to therapy.)

Things got better when I got to MyU and could visit the counseling center.

Things got better still after I was diagnosed with PTSD and referred to a trauma specialist who helped me work through the emotions attached to the past abuse.

Things got even better after I went on medication.  (One of my initial worries about going on meds is that I would forgot to take them on a regular basis.  I have to admit, I still do forget after all of this time–but it’s still a huge help.)  I was on Celexa at first; switching to Lexapro got rid of the side effects that made me hate meds in the first place.

Things got even better still after I got a protective order that severely limited UnlikelyDad’s ongoing harassment.

The final piece of the puzzle was a new cognitive behavioral therapy technique that my therapist introduced this summer.

For the first time in…my whole life, maybe?…I feel…normal.  I think.  Is this what normal feels like?

I wish I hadn’t waited until almost-40 to get help.  I wish I could have felt like this in my 20’s.  Don’t get me wrong, I’ve accomplished a lot in my lifetime, but I can’t imagine how much more I would have accomplished had I not suffered from depression.

I blog about depression because I want others who suffer from the disease to know that they are not alone.

I blog about depression because I want people to know that there is hope.

I blog about depression because it is treatable.  Even if you can’t take meds (I have a friend who’s had bad reactions with all of the meds he’s tried), there are things you can do to ameliorate the symptoms.

I blog about depression because I want others to get help.  To everyone who’s out there feeling like you don’t have the mental energy to get out of bed…who feels like you are worse than a lowly worm, because at least worms are good for the soil…who mires in the blackest abyss of depression…THERE IS HOPE.  Please, get help.

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