10.11.2011
Life has too many distractions
Sometimes I wonder how I'm ever going to get everything done....maybe more than sometimes. I can feel like I'm finally making a dent, and then something happens like my dog spraining her leg. :-( Tonight she's not much better after two days on anti-inflammatories, so tomorrow we get to get X-rays and make sure that nothing worse is going on. Poor puppy.
I planned on applying for an award for students in their final year of study. My department's deadline is the day after tomorrow. I at least had most of the stuff ready to go, but I need a letter from my advisor. I emailed her about it, and her response was that the one roadblock she could see was a lack of publications (not entirely my fault, thankyouverymuch), but that I had everything else. So hopefully that means she's writing me a letter so we can get that put in as well. If by some miracle, I were to get it, that would be $5000 more in the bank, which would be awesome.
Ok. Now I'm actually starting to freak out about finding a post-doc. I need to send out letters a month ago. Oops. I realize that one is totally on me, but this is where the title of this post comes in - sooo many productive distractions in my life, or other things I have to deal with emotionally as well. Teaching, proctoring, book chapter that got "put on hold," puppy troubles, etc., etc., etc. Everyone keeps telling me it'll be fine, but it'll only be fine if I get up off my butt and do something about it. And yet, here I am, watching my dog limp around and realizing that most of tomorrow will be dealing with her. Sigh. One of these days....
Another distraction has been all these stupid vaccine things. Apparently this is one cause I am passionate about. I actually had to all but block someone on Facebook because the links she was posting made me so angry that I would waste too much time trying to argue and refute them. I need that time to do other things. Like blog instead of write my thesis, apparently.
Speaking of thesis, the other girl in my lab asked me yesterday how many pages my thesis was going to be. I told her probably close to 300 with all the tables and her jaw hit the ground. Apparently a friend of mine's was only 80 pages, who got the same degree as me. However, I have sooo much data. This is why it's taking me forever and ever...
10.03.2011
All for naught?
My thesis is going to be Long. I just incorporated one microarray table, and doubled the size of a chapter. It will easily be 300 pages. Easily. The thing that worries me is that some of it may never see the light of day outside of my thesis. I'm not sure anyone is going to take over my project when I'm gone, so the couple of experiments that have been pains that need to be done for publication may never happen. I have watched some of my former labmates' projects plod along and go nowhere, even though at least one of them was close to ready. I even did some experiments for that one, and still not out. Maybe it's just that my advisor is really good at sitting on data. Ugh. Either way, it worries me that I have done all this work for nearly nothing. Yay....
9.29.2011
Social butterfly
It really feels like Friday. Maybe because I wish it was Friday. It has been a long week, and yet somehow I still feel so behind. I think that is going to be a general principal of this semester.
Part of it has been that I'm doing a lot of social activities this week, which is unusual. Most of my friends have already moved away, and the rest know that I'm writing and don't bother me as often. BUT, one friend of mine is getting married this weekend, so we had a "bachelorette dinner" on Monday. And then yesterday I got to see Alton Brown speak for free. How could you pass that up?? It was hilarious! He liked making fun of grad students a lot, and was dead on about how there's nothing in this town. "It's not even really a town...just a college." Hence the name, I guess. And then this weekend, on Friday is a little wedding reception...and Saturday, a friend of mine who graduated a few years ago is coming to visit! It will be a busy time.
Maybe Sunday I can get some more work done. I'm not sure what my advisor is thinking for getting the book chapter done. I thought it was due, well, tomorrow, but I am pretty darn sure that won't happen. I could maybe see it happening the end of next week if she works non-stop on it. But, we have a good 1/3 or more to overhaul, then cleaning it up and referencing and incorporating figures...there's no way that will get done by tomorrow, even if we both don't sleep. At least she likes my work: yesterday she told me that, "I like what you did with what I sent you on Friday." So many compliments on this book chapter. That either means that my writing has improved over time, OR that I write better when it's not about my own work.
Part of it has been that I'm doing a lot of social activities this week, which is unusual. Most of my friends have already moved away, and the rest know that I'm writing and don't bother me as often. BUT, one friend of mine is getting married this weekend, so we had a "bachelorette dinner" on Monday. And then yesterday I got to see Alton Brown speak for free. How could you pass that up?? It was hilarious! He liked making fun of grad students a lot, and was dead on about how there's nothing in this town. "It's not even really a town...just a college." Hence the name, I guess. And then this weekend, on Friday is a little wedding reception...and Saturday, a friend of mine who graduated a few years ago is coming to visit! It will be a busy time.
Maybe Sunday I can get some more work done. I'm not sure what my advisor is thinking for getting the book chapter done. I thought it was due, well, tomorrow, but I am pretty darn sure that won't happen. I could maybe see it happening the end of next week if she works non-stop on it. But, we have a good 1/3 or more to overhaul, then cleaning it up and referencing and incorporating figures...there's no way that will get done by tomorrow, even if we both don't sleep. At least she likes my work: yesterday she told me that, "I like what you did with what I sent you on Friday." So many compliments on this book chapter. That either means that my writing has improved over time, OR that I write better when it's not about my own work.
9.27.2011
Ninja submission
Apparently, my paper was sneak-submitted. We never got a notification that it got submitted, but my advisor says it's out for review. Submitted is submitted in my book.
I have no idea how this book chapter is going; my advisor sent me a bunch last weekend to work on, which I did, but now I'm kind of waiting on more from her. If it's not done on time, I don't think it will be my fault.
Chapter 3 is coming along swimmingly. Chapter 4 will be a pain in the rear, but has to be done, and Chapter 5 (Conclusions and Future Directions) could be kind of fun. Then I just have a bunch of appendices to deal with. Slowly but surely I'm making progress. I think if I can get a bunch done in the next week or so, I will ask my advisor if maybe I could set a real date. You know, the kind where you get to defend.
All the rest of it is the most intimidating part. Finding a job especially, and figuring out where to live. Meh.
I have no idea how this book chapter is going; my advisor sent me a bunch last weekend to work on, which I did, but now I'm kind of waiting on more from her. If it's not done on time, I don't think it will be my fault.
Chapter 3 is coming along swimmingly. Chapter 4 will be a pain in the rear, but has to be done, and Chapter 5 (Conclusions and Future Directions) could be kind of fun. Then I just have a bunch of appendices to deal with. Slowly but surely I'm making progress. I think if I can get a bunch done in the next week or so, I will ask my advisor if maybe I could set a real date. You know, the kind where you get to defend.
All the rest of it is the most intimidating part. Finding a job especially, and figuring out where to live. Meh.
9.23.2011
Inbox: full; Outbox: slowly accumulating
So much to do, so little time!
The book chapter is due soon, but supposedly my advisor is giving me a full draft soon to work on while she's out of town this weekend. Hopefully that will be one more thing off the list soon.
My (nearly) re-submitted paper got converted to thesis-format a couple days ago, and it felt like I'd written an entire chapter, even though it took only 2 years to write! ;-)
The other chapters are coming along, but they are infinitely harder. I find myself fine-tuning figures to at least be productive, but really I'm procrastinating thinking up things to write. I will have to buckle down and get that under control soon.
I sent my ideas for postdocs and a couple pieces of possible letters to send them to a former student from this lab, and she approved, so maybe, just maybe I will have the courage to approach my advisor about it. I'm not sure why, but this is the scariest part for me. Part of it is probably that I don't want her judging my choices, part of it is that I'm scared about actually putting myself out there, and part of it is that I really don't want to leave a certain someone behind here. But, I really don't have a whole lot of other options, so I had better get started on that soon, as well.
I found out that someone that is one year behind me, and someone that is two years behind me, will likely be walking and getting their degrees with me. That feels very discouraging. It's hard not to compare yourself to other people. I wouldn't have traded this extra time in State College for anything, but at the same time, I feel like I didn't work hard enough or something, even though I know that's not true.
The book chapter is due soon, but supposedly my advisor is giving me a full draft soon to work on while she's out of town this weekend. Hopefully that will be one more thing off the list soon.
My (nearly) re-submitted paper got converted to thesis-format a couple days ago, and it felt like I'd written an entire chapter, even though it took only 2 years to write! ;-)
The other chapters are coming along, but they are infinitely harder. I find myself fine-tuning figures to at least be productive, but really I'm procrastinating thinking up things to write. I will have to buckle down and get that under control soon.
I sent my ideas for postdocs and a couple pieces of possible letters to send them to a former student from this lab, and she approved, so maybe, just maybe I will have the courage to approach my advisor about it. I'm not sure why, but this is the scariest part for me. Part of it is probably that I don't want her judging my choices, part of it is that I'm scared about actually putting myself out there, and part of it is that I really don't want to leave a certain someone behind here. But, I really don't have a whole lot of other options, so I had better get started on that soon, as well.
I found out that someone that is one year behind me, and someone that is two years behind me, will likely be walking and getting their degrees with me. That feels very discouraging. It's hard not to compare yourself to other people. I wouldn't have traded this extra time in State College for anything, but at the same time, I feel like I didn't work hard enough or something, even though I know that's not true.
9.16.2011
Some people's kids...need their shots.
Everyone has an issue that really gets under their skin in politics. For me, the two general issues I get passionate about are science and with education. No big surprise there. One of the things that bothers me the most is this whole vaccine issue. From the Bachmann-Perry crazy at the debate this week to the whole "autism-by-vaccine" thing to just parents thinking it's ok not to vaccinate their children for potentially deadly diseases, I get more than a little frustrated. If I wasn't trying to write a book chapter, and a giant dissertation, along with supposedly finding a place to go when I'm done, I would find a bunch of good reference material and write a well-reasoned essay airing the bulk of my frustrations.
Because that's not possible right now, I will just say:
1) Vaccines are safer than driving cars. Your child will not become "mentally retarded" from a vaccine. At worst, they will probably be sore or get a rash that will go away. Extreme side effects are very rare.
2) Enough people refusing to vaccinate promotes re-emerging pathogens showing up again, such as the whooping cough outbreak in California last year. I've said this before - I suppose other people's ignorance keeps me employed, but that doesn't mean I have to be ok with it.
3) Bravo to the scientists needling back for once and offering to pay a reward for the mom that Bachmann described during the debate. Unfortunately, the damage is mostly done, because now parents have a negative image of vaccines drilled into their brains by the media. It is so unfortunate that one really loud person can negate the work of thousands of qualified scientists. It happens so often, like with climate change or evolution. If you wanted to be fair and show both sides of the issue, you should weight those sides by which has the greatest scientific merit. But clearly, I don't make the rules.
After that short digression, I still would love to understand why it is so easy to get so mis-educated. Choosing not to vaccinate against things like whooping cough and measles is inviting trouble, either by increasing the probability your own child will get sick (and possibly die), or that they will cause another child to get sick (and possibly die). But if you really think vaccines are more dangerous than measles and whooping cough, by all means, let your kids get sick. Then maybe I can get funding.
Because that's not possible right now, I will just say:
1) Vaccines are safer than driving cars. Your child will not become "mentally retarded" from a vaccine. At worst, they will probably be sore or get a rash that will go away. Extreme side effects are very rare.
2) Enough people refusing to vaccinate promotes re-emerging pathogens showing up again, such as the whooping cough outbreak in California last year. I've said this before - I suppose other people's ignorance keeps me employed, but that doesn't mean I have to be ok with it.
3) Bravo to the scientists needling back for once and offering to pay a reward for the mom that Bachmann described during the debate. Unfortunately, the damage is mostly done, because now parents have a negative image of vaccines drilled into their brains by the media. It is so unfortunate that one really loud person can negate the work of thousands of qualified scientists. It happens so often, like with climate change or evolution. If you wanted to be fair and show both sides of the issue, you should weight those sides by which has the greatest scientific merit. But clearly, I don't make the rules.
After that short digression, I still would love to understand why it is so easy to get so mis-educated. Choosing not to vaccinate against things like whooping cough and measles is inviting trouble, either by increasing the probability your own child will get sick (and possibly die), or that they will cause another child to get sick (and possibly die). But if you really think vaccines are more dangerous than measles and whooping cough, by all means, let your kids get sick. Then maybe I can get funding.
Boring but crazy
It's been a boring, but crazy week, if that makes sense.
I've felt pretty busy, but also that I haven't gotten that much done. Most of that is probably from teaching and proctoring. Proctoring is the most pointless task ever; it feels like the biggest time-waster. I showed up Tuesday morning, and half the proctors weren't there. That meant the prof and one other person were taking the exams as the students finished, leaving me to watch over 300 students. Hah. As if I would have the ability to catch anyone cheating, and as if I cared at that point anyway...
Teaching is more fun; I have pretty good kids, and we get through the class typically in one piece. There is nothing quite as rewarding as seeing them understand a concept for the first time. But it was lab report week, so I graded 75 lab reports on Tuesday night. The prof has each of the two TAs grade all of one lab report so the grading is consistent. In the other section, I found my first plagiarists of the season. One lab partner did the work, the other photocopied the lab partner's hand-drawn graphs, did no calculations, and then the two partners' reports were clipped together. If you were going to photocopy the graphs, at least have the intelligence to put the two copies in different parts of the stack so at least there might be a lower chance of me recognizing it.
I really thought we were going to submit the paper this week, and we got it ready, but for some reason it hasn't gone out. I don't quite understand, but I think it has something to do with our collaborator's password for the journal submission not working...so hopefully one of these days....
But in other writing news, the stuff I sent my advisor for the book chapter we're writing, she finally read in the middle of the week, and she told me that "it's off to a great start!" That kind of made my day. There's still a lot to do, but I think I have about half of my work done, and then I will just have to mess with the figures. I also spent a lot of time re-comparing some data that I'd lost the comparisons of before, so hopefully something useful comes out of that.
I've felt pretty busy, but also that I haven't gotten that much done. Most of that is probably from teaching and proctoring. Proctoring is the most pointless task ever; it feels like the biggest time-waster. I showed up Tuesday morning, and half the proctors weren't there. That meant the prof and one other person were taking the exams as the students finished, leaving me to watch over 300 students. Hah. As if I would have the ability to catch anyone cheating, and as if I cared at that point anyway...
Teaching is more fun; I have pretty good kids, and we get through the class typically in one piece. There is nothing quite as rewarding as seeing them understand a concept for the first time. But it was lab report week, so I graded 75 lab reports on Tuesday night. The prof has each of the two TAs grade all of one lab report so the grading is consistent. In the other section, I found my first plagiarists of the season. One lab partner did the work, the other photocopied the lab partner's hand-drawn graphs, did no calculations, and then the two partners' reports were clipped together. If you were going to photocopy the graphs, at least have the intelligence to put the two copies in different parts of the stack so at least there might be a lower chance of me recognizing it.
I really thought we were going to submit the paper this week, and we got it ready, but for some reason it hasn't gone out. I don't quite understand, but I think it has something to do with our collaborator's password for the journal submission not working...so hopefully one of these days....
But in other writing news, the stuff I sent my advisor for the book chapter we're writing, she finally read in the middle of the week, and she told me that "it's off to a great start!" That kind of made my day. There's still a lot to do, but I think I have about half of my work done, and then I will just have to mess with the figures. I also spent a lot of time re-comparing some data that I'd lost the comparisons of before, so hopefully something useful comes out of that.
9.12.2011
Catching up.
I know, it's been forever...I've been busy!
The humidity and rain lately has been ridiculous! I realize we didn't get as much rain as the eastern side of PA, but still...it has been nearly impossible for me to breathe in lab. On Friday, as soon as I went in the lab I'd start coughing and my sinuses would ache. I went and sat somewhere on the first floor of the building where there was a better A/C drying out the air and felt great, then would go back upstairs to do a few things and would start coughing again. I don't know how they "fixed" our A/C, but I would venture to guess that it didn't work. Ugh.
In other news, I convinced my advisor to list me first on the paper that I believe is finally getting submitted TODAY! I'm not sure what I will do if it doesn't get accepted this time, but it will involve some kind of destruction. It only took my collaborator 1-1.5 weeks to give us 4 proofreading edits...sigh.
We also started working hard-core on the book chapter a couple weeks ago. I have about 12 pages of text and the start of a few figures that I sent to my advisor to start combing through. That's due at the end of the month, so hopefully that will go smoothly.
I need to start talking to my advisor about postdoc ideas and start seriously looking. I also want to try and defend by the first week or so in November, so I need to get writing. I also wish some of my experiments would just work already, but I realize that is too much to ask. Sigh....
The humidity and rain lately has been ridiculous! I realize we didn't get as much rain as the eastern side of PA, but still...it has been nearly impossible for me to breathe in lab. On Friday, as soon as I went in the lab I'd start coughing and my sinuses would ache. I went and sat somewhere on the first floor of the building where there was a better A/C drying out the air and felt great, then would go back upstairs to do a few things and would start coughing again. I don't know how they "fixed" our A/C, but I would venture to guess that it didn't work. Ugh.
In other news, I convinced my advisor to list me first on the paper that I believe is finally getting submitted TODAY! I'm not sure what I will do if it doesn't get accepted this time, but it will involve some kind of destruction. It only took my collaborator 1-1.5 weeks to give us 4 proofreading edits...sigh.
We also started working hard-core on the book chapter a couple weeks ago. I have about 12 pages of text and the start of a few figures that I sent to my advisor to start combing through. That's due at the end of the month, so hopefully that will go smoothly.
I need to start talking to my advisor about postdoc ideas and start seriously looking. I also want to try and defend by the first week or so in November, so I need to get writing. I also wish some of my experiments would just work already, but I realize that is too much to ask. Sigh....
8.31.2011
Slowly but surely.
Checking in to see how I did with my to-do list last week:
1. Finish rough draft of intro chapter
Done and done. I'm going to leave this alone for awhile, and revisit when more is written
2. Keep working on book chapter
Got a fair amount done, still a lot to be done because it's due at the end of the month.
3. Get as much done on Chapter 3 and 4 as possible, but this will be tricky in general
I'm not willing to cross this off yet - I started to outline possible ideas, but it's hard...
4. Keep looking for people to work for.
Still have more people to look for- after awhile, everyone's work sounds the same...sigh.
5. Try to get some of this cloning to work
Got some cloning to work- now I just hope the construct works---will find out today and tomorrow, I suppose.
6. Control for conjugation
I have done the control, now I just need to figure out if it worked....
7. Design more oligos for transcription
Just a couple more sets to design, and I can put the order in.
I guess I did ok last week! Still soooo much to accomplish, though.
For the next couple days, I just have some experiments to check for the plasmid constructs I made, and then a lot of computery work before I head to Newport News for my friends wedding. :-)
Done and done. I'm going to leave this alone for awhile, and revisit when more is written
Got a fair amount done, still a lot to be done because it's due at the end of the month.
3. Get as much done on Chapter 3 and 4 as possible, but this will be tricky in general
I'm not willing to cross this off yet - I started to outline possible ideas, but it's hard...
Still have more people to look for- after awhile, everyone's work sounds the same...sigh.
Got some cloning to work- now I just hope the construct works---will find out today and tomorrow, I suppose.
I have done the control, now I just need to figure out if it worked....
Just a couple more sets to design, and I can put the order in.
I guess I did ok last week! Still soooo much to accomplish, though.
For the next couple days, I just have some experiments to check for the plasmid constructs I made, and then a lot of computery work before I head to Newport News for my friends wedding. :-)
8.22.2011
Stacks and stacks
I printed out what I've been working on lately, and it's a substantial amount of paper I suppose. I printed the intro chapter, the second paper (Chapter 3), and the eight pages of the book chapter I've spat out so far.
Revised goals for the week:
1. Finish rough draft of intro chapter
2. Keep working on book chapter
3. Get as much done on Chapter 3 and 4 as possible, but this will be tricky in general
4. Keep looking for people to work for.
5. Try to get some of this cloning to work
6. Control for conjugation
7. Design more oligos for transcription
8. I got my mass spec back, and it actually makes some sense...what to do with this information now eludes me, of course.
Revised goals for the week:
1. Finish rough draft of intro chapter
2. Keep working on book chapter
3. Get as much done on Chapter 3 and 4 as possible, but this will be tricky in general
4. Keep looking for people to work for.
5. Try to get some of this cloning to work
6. Control for conjugation
7. Design more oligos for transcription
8. I got my mass spec back, and it actually makes some sense...what to do with this information now eludes me, of course.
8.21.2011
The LeStrange Gringott's vault
That's what my work feels like. You know, when you touch something and it multiplies into many more of the same thing. I swear I got a lot of writing done Friday and today. But it just feels like there is so much more to do!!
I actually got about 8 pages of the book chapter done, which I'm pretty proud of. I have also written a couple more sections of my intro chapter. I think I need to print what I have so far and figure out what is left. I also need to deal with the other papers---so much easier said than done.
I actually got about 8 pages of the book chapter done, which I'm pretty proud of. I have also written a couple more sections of my intro chapter. I think I need to print what I have so far and figure out what is left. I also need to deal with the other papers---so much easier said than done.
8.17.2011
Time flies...
....even when you're not having that much fun. Ack. How is it mid-August already!?
My to-do lists aren't getting shorter fast enough. I think I need to find a way to do less in lab and more writing because I want to defend before my boyfriend might end up on a geological expedition of sorts in November. It'd be nice to spend a few days with him thesis-free, and also for him to be there to help celebrate my defense. Fingers crossed. I also need some experiments to work. Sheesh.
However, we are at least aiming to submit (re-submit) the paper this week before the boss heads out for another vacation. So...yay! Maybe this time it will be accepted. Our collaborator in Argentina said that it was "beautifully written." After putting all this extra work in , it's tempting to ask to be listed first, but I'm unsure of the politics of it all. Hm...
Things I need to accomplish in the next week:
Writing:
1. Read and write for the book chapter as much as possible. This is technically due at the end of September, which means the advisor and I need to start going back and forth soon. It will be an appendix in my thesis.
2. Work on organization of the other two papers/thesis chapters. There are so many different ways to package the data, and I need to come up with the best option.
3. Draft more emails to send to faculty for post-docs so that advisor can check them out when she gets back from vacation #2.
Lab:
1. Complementation or die!
2. Look at supernatants of strains for possible differential expression of things like T3SS effectors.
Easier said than done, by the way....hard to concentrate the supernatants, even in TCA.
3. Should be getting back mass spec data on my differentially expressed protein.
4. Should also be getting some RNA-seq data on my favorite mutant to help a) bolster the array data we already have and b) possibly help us identify SigE-regulated sRNAs.
My to-do lists aren't getting shorter fast enough. I think I need to find a way to do less in lab and more writing because I want to defend before my boyfriend might end up on a geological expedition of sorts in November. It'd be nice to spend a few days with him thesis-free, and also for him to be there to help celebrate my defense. Fingers crossed. I also need some experiments to work. Sheesh.
However, we are at least aiming to submit (re-submit) the paper this week before the boss heads out for another vacation. So...yay! Maybe this time it will be accepted. Our collaborator in Argentina said that it was "beautifully written." After putting all this extra work in , it's tempting to ask to be listed first, but I'm unsure of the politics of it all. Hm...
Things I need to accomplish in the next week:
Writing:
1. Read and write for the book chapter as much as possible. This is technically due at the end of September, which means the advisor and I need to start going back and forth soon. It will be an appendix in my thesis.
2. Work on organization of the other two papers/thesis chapters. There are so many different ways to package the data, and I need to come up with the best option.
3. Draft more emails to send to faculty for post-docs so that advisor can check them out when she gets back from vacation #2.
Lab:
1. Complementation or die!
2. Look at supernatants of strains for possible differential expression of things like T3SS effectors.
Easier said than done, by the way....hard to concentrate the supernatants, even in TCA.
3. Should be getting back mass spec data on my differentially expressed protein.
4. Should also be getting some RNA-seq data on my favorite mutant to help a) bolster the array data we already have and b) possibly help us identify SigE-regulated sRNAs.
8.12.2011
Yep. Gonna be so much fun.
A lot has happened in the last week, and yet not enough has gotten done.
First, I will be teaching next semester. My advisor's small grant got dried up paying for me and the other student in the spring and summer. I got so many apologies from her. She tried to ask my collaborator to pay for me, but apparently he can't either, so teaching it is. We chatted on the phone while she was at a meeting last week, and basically said that the professor who changed the no-teaching-in-your-defending-semester policy likes to punish faculty that are struggling to get funding, and "is just a dick." Sigh. But, I gave her a couple suggestions for which classes might be easier for me to teach. My first choice is a 400-level micro class that I taught my second year. The prof who teaches it is really awesome, and is there during lab. It's less outside work than the 100-level labs because I don't have to design my own quizzes or anything, I just have to grade 10 lab reports and show up ready to answer questions. Hopefully I will get that one. But still. Boo.
I also presented my work at my collaborator's group meeting. It took about an hour, but I got a few decent suggestions of things to do, which is the good/bad thing about group meetings. You get feedback, but then you have a mountain of other things to test, and feel like you have no time to accomplish it in. I guess that's what working Saturdays are for. :-(
I think that's plenty for now. I have plenty more crazy going on in my life, but these are the initial insanity. Figuring out what to do next semester can wait for its own post....
First, I will be teaching next semester. My advisor's small grant got dried up paying for me and the other student in the spring and summer. I got so many apologies from her. She tried to ask my collaborator to pay for me, but apparently he can't either, so teaching it is. We chatted on the phone while she was at a meeting last week, and basically said that the professor who changed the no-teaching-in-your-defending-semester policy likes to punish faculty that are struggling to get funding, and "is just a dick." Sigh. But, I gave her a couple suggestions for which classes might be easier for me to teach. My first choice is a 400-level micro class that I taught my second year. The prof who teaches it is really awesome, and is there during lab. It's less outside work than the 100-level labs because I don't have to design my own quizzes or anything, I just have to grade 10 lab reports and show up ready to answer questions. Hopefully I will get that one. But still. Boo.
I also presented my work at my collaborator's group meeting. It took about an hour, but I got a few decent suggestions of things to do, which is the good/bad thing about group meetings. You get feedback, but then you have a mountain of other things to test, and feel like you have no time to accomplish it in. I guess that's what working Saturdays are for. :-(
I think that's plenty for now. I have plenty more crazy going on in my life, but these are the initial insanity. Figuring out what to do next semester can wait for its own post....
8.04.2011
The fun just doesn't stop.
I found out yesterday that, in addition to writing a massive dissertation, looking for (and hopefully interviewing for) a postdoc, finishing up experiments, presumably moving, and hopefully getting to go home for a few days, I will be teaching this semester!
It used to be departmental policy that if your advisor is lacking the funds to pay your stipend, you teach...except in the semester you defend. The new "assistant dept. head of graduate students" has decided to change this policy because they're desperate for TAs. So not fair. I may still be too angry to really talk about it.
It used to be departmental policy that if your advisor is lacking the funds to pay your stipend, you teach...except in the semester you defend. The new "assistant dept. head of graduate students" has decided to change this policy because they're desperate for TAs. So not fair. I may still be too angry to really talk about it.
8.02.2011
Not bad...
I'm actually pretty proud of my work today...I even added to one of the goals, even if I didn't quite get to a couple of them yet. I also accidentally took an hour nap in the middle of the afternoon, and had to walk the dog and such in the evening. Not too shabby.
1. Take Roo to the park in the morning, then come back and run myself.
2. Laundry
3. Clean kitchen
4. Read/write about P. syringae AlgU for intro chapter
also read/wrote about V. cholerae RpoE for intro chapter
5. Read about 2-3 potential postdoc advisor's work, finish draft of at least one cover email.
6. Start discussion section for RseAB paper
I started, but I won't promise that it's any good...
7. Work on some kind of alignment figure for intro chapter
8. Lab: overnights for colony PCR, finish destaining gel, change ice
2. Laundry
3. Clean kitchen
5. Read about 2-3 potential postdoc advisor's work, finish draft of at least one cover email.
I started, but I won't promise that it's any good...
7. Work on some kind of alignment figure for intro chapter
Busy busy.
Today's ambitious to-do list...I'll check in later tonight or tomorrow to see how I did:
1. Take Roo to the park in the morning, then come back and run myself.
2. Laundry
3. Clean kitchen
4. Read/write about P. syringae AlgU for intro chapter
5. Read about 2-3 potential postdoc advisor's work, finish draft of at least one cover email.
6. Start discussion section for RseAB paper
7. Work on some kind of alignment figure for intro chapter
8. Lab: colony PCR, finish destaining gel, change ice
1. Take Roo to the park in the morning, then come back and run myself.
2. Laundry
3. Clean kitchen
4. Read/write about P. syringae AlgU for intro chapter
5. Read about 2-3 potential postdoc advisor's work, finish draft of at least one cover email.
6. Start discussion section for RseAB paper
7. Work on some kind of alignment figure for intro chapter
8. Lab: colony PCR, finish destaining gel, change ice
8.01.2011
Floodwaters
Sunday, I came in to start prepping outer membranes from my various strains. Bordetella bronchiseptica takes most of the day to lyse, so I figured I could get some writing done between snap-freezes.
Apparently the building had other plans.
I walked into the lab, got to my bench and stopped short. The area around my bench, which is in the middle of the room, had a lake, with no bridge to cross to my desk. I looked up. No water on the ceiling. I looked under the sink. The floor was wet, but nothing near the pipes was. Where had this water come from? There was no trail of trickling water coming from anywhere. My bench is the lowest point in the lab, so no matter where the flood starts, it ends up there, but there was no evidence water had traveled from anywhere else.
It was Sunday, so I called the physical plant emergency number, and someone came over to shop-vac it up pretty quickly. As they did, we noticed that water was seeping out from under the cabinets. Two plumbers came, and couldn't figure out where the water was coming from. After they left, it started seeping out slowly again, so I called again. The plumber cleaned up under the cabinets a little more thoroughly, but still couldn't figure out where the water had come from.
He had some explanation for when it might have happened, but we're still not sure how it got to where it did without leaving any obvious trail to follow:
This building apparently had a huge water problem on Saturday. The elevators and autoclave rooms had water EVERYWHERE. You can still see the water spots in the elevator today, actually. He called the person in charge of that clean-up, who said that there was only water up to our door. But, he said that the guy who did that 'doesn't go looking for extra work,' and quite possibly had not looked in our lab at my bench, so the water could have been sitting there since Saturday. But it still doesn't explain how it got there...sigh. Needless to say, everything took a lot longer yesterday, so even less got accomplished.
Apparently the building had other plans.
I walked into the lab, got to my bench and stopped short. The area around my bench, which is in the middle of the room, had a lake, with no bridge to cross to my desk. I looked up. No water on the ceiling. I looked under the sink. The floor was wet, but nothing near the pipes was. Where had this water come from? There was no trail of trickling water coming from anywhere. My bench is the lowest point in the lab, so no matter where the flood starts, it ends up there, but there was no evidence water had traveled from anywhere else.
It was Sunday, so I called the physical plant emergency number, and someone came over to shop-vac it up pretty quickly. As they did, we noticed that water was seeping out from under the cabinets. Two plumbers came, and couldn't figure out where the water was coming from. After they left, it started seeping out slowly again, so I called again. The plumber cleaned up under the cabinets a little more thoroughly, but still couldn't figure out where the water had come from.
He had some explanation for when it might have happened, but we're still not sure how it got to where it did without leaving any obvious trail to follow:
This building apparently had a huge water problem on Saturday. The elevators and autoclave rooms had water EVERYWHERE. You can still see the water spots in the elevator today, actually. He called the person in charge of that clean-up, who said that there was only water up to our door. But, he said that the guy who did that 'doesn't go looking for extra work,' and quite possibly had not looked in our lab at my bench, so the water could have been sitting there since Saturday. But it still doesn't explain how it got there...sigh. Needless to say, everything took a lot longer yesterday, so even less got accomplished.
7.30.2011
Late night "research"
I stayed up a little later than usual tonight, not out with friends, but actually being semi-productive after an evening of relaxing. I watched some video and read some about the work of someone I am interested in doing a postdoc with. I also drafted the beginnings of a cover email to inquire about job opportunities. I believe that is nearly 1/2 of one point on my checklist for the week!
I also wrote about 2 pages of my intro chapter today after reading a bunch of papers about my system in Pseudomonas aeruginosa. I will perhaps share some of what I learned tomorrow, or really later today, when it's not 1:40 am.
I also wrote about 2 pages of my intro chapter today after reading a bunch of papers about my system in Pseudomonas aeruginosa. I will perhaps share some of what I learned tomorrow, or really later today, when it's not 1:40 am.
7.29.2011
New work schedule
I'm glad that I got the motivation to do more writing when my advisor is gone. It gives me the chance to adjust to a new schedule without her watching me, which will perhaps give me the confidence to disappear more often once she is back. I have been working part-time and writing part time. Most days that means 6 hours work-3 hours writing, and hopefully some more in the evening (but not always...). But I have to leave lab- I am not that great at writing in lab. Data analysis is fine, but actually focusing on reading papers and writing is hard for me, when there is plenty to be done and people who may or may not ask me questions are everywhere on the edge of distracting me.
My (admittedly ambitious) goals for the next week are:
Writing:
1. Write the discussion section of my second paper.
2. Read a ton and write at least 10 more pages of my intro chapter (I currently have 11 pages written).
3. Start reading for the book chapter.
4. Draft cover email for at least 2 people I might be interested in doing a post-doc with.
Lab:
1. I have some membrane preps to do, possibly this weekend. These are for any westerns I still need to do, and also to get ready for mass spec.
2. Check the mutants I tried to make, should be ready Tuesday.
3. Start the process of trying to clone a couple of genes onto a plasmid as alternative method of complementation; though still not as useful as the phenotypic complementation I'm interested in getting someday, at least it is something.
4. Finish some microarray comparisons so I can present some ideas at the other lab's group meeting in a week and a half.
The other thing I have to confess, which I have mentioned before, is that this is all subject to change because I am really good at productive procrastination. I might not get one of these things done, but will get something else of value done instead. It's just how I am.
My (admittedly ambitious) goals for the next week are:
Writing:
1. Write the discussion section of my second paper.
2. Read a ton and write at least 10 more pages of my intro chapter (I currently have 11 pages written).
3. Start reading for the book chapter.
4. Draft cover email for at least 2 people I might be interested in doing a post-doc with.
Lab:
1. I have some membrane preps to do, possibly this weekend. These are for any westerns I still need to do, and also to get ready for mass spec.
2. Check the mutants I tried to make, should be ready Tuesday.
3. Start the process of trying to clone a couple of genes onto a plasmid as alternative method of complementation; though still not as useful as the phenotypic complementation I'm interested in getting someday, at least it is something.
4. Finish some microarray comparisons so I can present some ideas at the other lab's group meeting in a week and a half.
The other thing I have to confess, which I have mentioned before, is that this is all subject to change because I am really good at productive procrastination. I might not get one of these things done, but will get something else of value done instead. It's just how I am.
7.27.2011
Checklist fun
I posted a to-do list a couple weeks ago for while my advisor was gone. A couple things got added to it since, but let's see how I'm doing:
2. Apparently I need to start attending my collaborator's group meeting. Sounds like a little bit of a time waster at first, but maybe they'll have some good ideas for me.
Still sounds like a time-waster for the first week or two, but I am going to my first one today...wish me luck! I got a lot of data analysis and a handful of slides made to bring with me for when I do get to present my confusing work.
3. Send one protein for mass spec (and get the post-doc to help me).
Still have to talk to the post-doc about this one. I'm a little concerned because I think my advisor needs to ok something in order to pay for this...
4. Try and get this silly mutant made. First step: get it sub-cloned into something else. If E. coli could be rebellious, I have the leaders of the revolution right now.
I think I got through the subcloning part, but our sequencing facility isn't exactly awesome right now, and I only got back really degraded and useless sequence from sending my clones in. I guess all I can do is proceed forward with the allelic exchange and just hope it works.
5. WRITE. I agreed last Thursday to help write a book chapter on regulated proteolysis as an appendix to my thesis, so I guess everyone here might be learning a little more about that subject soon. :-)
Under this category is where something got added. My advisor sent me a draft of the paper that needs to be re-submitted (long story), and I did edit it and add back in all the references, plus some new ones, and I sent it back to her yesterday. Yay! So now I'm back to writing everything else...
6. Look for jobs. Sigh.
This one is where I have fallen short so far. I got sidetracked a week or so ago, and started looking for just teaching jobs because I still can't decide what I want to do eventually. But I think I should look for a post-doc first.
1. A couple more western blots (hopefully done soon?).
I just made more protein to hopefully wrap those up soon. We'll see once I present at the other lab's group meeting. Which leads me to....2. Apparently I need to start attending my collaborator's group meeting. Sounds like a little bit of a time waster at first, but maybe they'll have some good ideas for me.
Still sounds like a time-waster for the first week or two, but I am going to my first one today...wish me luck! I got a lot of data analysis and a handful of slides made to bring with me for when I do get to present my confusing work.
3. Send one protein for mass spec (and get the post-doc to help me).
Still have to talk to the post-doc about this one. I'm a little concerned because I think my advisor needs to ok something in order to pay for this...
4. Try and get this silly mutant made. First step: get it sub-cloned into something else. If E. coli could be rebellious, I have the leaders of the revolution right now.
I think I got through the subcloning part, but our sequencing facility isn't exactly awesome right now, and I only got back really degraded and useless sequence from sending my clones in. I guess all I can do is proceed forward with the allelic exchange and just hope it works.
5. WRITE. I agreed last Thursday to help write a book chapter on regulated proteolysis as an appendix to my thesis, so I guess everyone here might be learning a little more about that subject soon. :-)
Under this category is where something got added. My advisor sent me a draft of the paper that needs to be re-submitted (long story), and I did edit it and add back in all the references, plus some new ones, and I sent it back to her yesterday. Yay! So now I'm back to writing everything else...
6. Look for jobs. Sigh.
This one is where I have fallen short so far. I got sidetracked a week or so ago, and started looking for just teaching jobs because I still can't decide what I want to do eventually. But I think I should look for a post-doc first.
7.22.2011
Could what I use to prevent infection sometimes cause it?
I ran across this article today. It describes how a nasal spray was the cause of a mini-Burkholderia outbreak in a hospital in Denver. As a daily nasal spray user, I do not really like the sound of that. I take a nasal steroid and a nasal antihistimine to prevent myself from getting sinus and ear infections all the time, but if I'm introducing hard-to-treat bacteria into an already inflamed nose, I could run into problems.
This raises a bigger question, which is highlighted toward the end of this article: "'Nasal spray products are among the most widely used over-the-counter pharmaceuticals, but to date they are not required by the FDA to be sterile,' said Susan Dolan, one of the article’s authors." What else is not required to be sterile?
As a microbiologist, I know that it's not usually that beneficial to have things be entirely sterile. Most bacteria are good for you, or at least not bad for you. And if they don't seem to be actively helping you, many of them are just taking up physical space to prevent nastier bacteria from setting up shop. But, I also don't want to inject pathogens directly into my nasal cavity. So where do we draw the line? How do we decide what should be absolutely sterile, and when we need to just let the bacteria do their thing?
This raises a bigger question, which is highlighted toward the end of this article: "'Nasal spray products are among the most widely used over-the-counter pharmaceuticals, but to date they are not required by the FDA to be sterile,' said Susan Dolan, one of the article’s authors." What else is not required to be sterile?
As a microbiologist, I know that it's not usually that beneficial to have things be entirely sterile. Most bacteria are good for you, or at least not bad for you. And if they don't seem to be actively helping you, many of them are just taking up physical space to prevent nastier bacteria from setting up shop. But, I also don't want to inject pathogens directly into my nasal cavity. So where do we draw the line? How do we decide what should be absolutely sterile, and when we need to just let the bacteria do their thing?
7.21.2011
I heart the library.
I definitely forgot how much more productive I am at writing in the library than I am in lab. In lab, people come and ask me questions, or I feel compelled to stuff tips or do experiments. I can get so much more accomplished without all that extra distraction around. Also, there is less mold, heat, and humidity in the library than in lab. And, strangely enough, I really love the smell of old books. I may be spending considerably more time here in the near future.
Mural of blots
Firstly, sometime after midnight Monday night, my advisor actually sent me the paper to work on (from vacation?), so I have some referencing to do soon. But at least it will get done!
I have made science into art. Well, not really...but I printed out all my western blots from this summer and taped them up on the chalkboard so I could see what differences we're interested in are always there (reproducible) vs. some that only show up occasionally, and have about four major differences to take to my collaborator's lab meeting and ask about. Now I just have to convince the postdoc my advisor and her husband share to take me down to the mass spec facility.
I'm afraid to jinx it, but I will say that my cloning looks more promising than it has in awhile- it would be great to make this construct, and for it to actually work to make my mutant, but three years of failure on that front has taught me not to hold my breath. I realize it's not true, but sometimes it feels like there's more superstition to science than there should be. As in, you have to make the appropriate sacrifices to the cloning gods, and do things during the proper phase of the moon wearing your lucky socks or something.
I have spent a lot of this week helping a younger student work on her comprehensive proposal, and helping my boyfriend's sister with her cover letter to get a job in microbiology. That all qualifies as writing, right? I'm hoping this afternoon I can get a couple good hours in at the library before celebrating the one-year anniversary of my boyfriend and my first date. Last night, I went to a send-off dinner for someone else in my class who is moving to CA to get a professional masters in business of sorts, and went to the defense of someone else in my class. Bittersweet on so many levels. I think most of us thought I would be one of the first done. I peaked early, though, and the last couple years have been tough going in the lab. We have all noticed that research either stalls early or late for most of us; I'm lucky enough for it to have gone really well for about 3.5 years, and then the last 2 have been rough, which I believe (though biased) is harder to deal with, because you're so anxious to be done while things aren't working.
Keep your fingers crossed for my mutants!
I have made science into art. Well, not really...but I printed out all my western blots from this summer and taped them up on the chalkboard so I could see what differences we're interested in are always there (reproducible) vs. some that only show up occasionally, and have about four major differences to take to my collaborator's lab meeting and ask about. Now I just have to convince the postdoc my advisor and her husband share to take me down to the mass spec facility.
I'm afraid to jinx it, but I will say that my cloning looks more promising than it has in awhile- it would be great to make this construct, and for it to actually work to make my mutant, but three years of failure on that front has taught me not to hold my breath. I realize it's not true, but sometimes it feels like there's more superstition to science than there should be. As in, you have to make the appropriate sacrifices to the cloning gods, and do things during the proper phase of the moon wearing your lucky socks or something.
I have spent a lot of this week helping a younger student work on her comprehensive proposal, and helping my boyfriend's sister with her cover letter to get a job in microbiology. That all qualifies as writing, right? I'm hoping this afternoon I can get a couple good hours in at the library before celebrating the one-year anniversary of my boyfriend and my first date. Last night, I went to a send-off dinner for someone else in my class who is moving to CA to get a professional masters in business of sorts, and went to the defense of someone else in my class. Bittersweet on so many levels. I think most of us thought I would be one of the first done. I peaked early, though, and the last couple years have been tough going in the lab. We have all noticed that research either stalls early or late for most of us; I'm lucky enough for it to have gone really well for about 3.5 years, and then the last 2 have been rough, which I believe (though biased) is harder to deal with, because you're so anxious to be done while things aren't working.
Keep your fingers crossed for my mutants!
7.18.2011
"I'm all alone....all by myself"
My advisor left for a 2-week vacation. She was supposed to send me the latest draft of my paper so I can add the references in while she's gone. Did she? Ha. Maybe I'll email her at some point, but I doubt I will hear from her these first two weeks or so. I need one of those vacation things. Going to weddings doesn't count- I need something relaxing!
Things to do while she's away:
1. A couple more western blots (hopefully done soon?).
2. Apparently I need to start attending my collaborator's group meeting. Sounds like a little bit of a time waster at first, but maybe they'll have some good ideas for me.
3. Send one protein for mass spec (and get the post-doc to help me).
4. Try and get this silly mutant made. First step: get it sub-cloned into something else. If E. coli could be rebellious, I have the leaders of the revolution right now.
5. WRITE. I agreed last Thursday to help write a book chapter on regulated proteolysis as an appendix to my thesis, so I guess everyone here might be learning a little more about that subject soon. :-)
6. Look for jobs. Sigh.
Things to do while she's away:
1. A couple more western blots (hopefully done soon?).
2. Apparently I need to start attending my collaborator's group meeting. Sounds like a little bit of a time waster at first, but maybe they'll have some good ideas for me.
3. Send one protein for mass spec (and get the post-doc to help me).
4. Try and get this silly mutant made. First step: get it sub-cloned into something else. If E. coli could be rebellious, I have the leaders of the revolution right now.
5. WRITE. I agreed last Thursday to help write a book chapter on regulated proteolysis as an appendix to my thesis, so I guess everyone here might be learning a little more about that subject soon. :-)
6. Look for jobs. Sigh.
7.16.2011
"What happens in there?"
Thursday, as I was leaving lab, an older couple was sitting on a bench outside my building.
The gentleman says, "Young lady, I have noticed that everyone that comes out that door doesn't look happy - what happens in there?" I replied, "It's a biochemistry building - we're all grad students." His wife interjects, "So - a lot of work."
The gentleman comes back, "But why does NO one look happy?" Instead of all the jaded, cynical quips I could give about grad school, I decide to go with, "Well, we're all inside working on this beautiful day." And he chuckles, and says something like, "Well, when you're retired like us..."
It says something, though, when someone notices that EVERYONE that comes out of the biochemistry building looks unhappy. Maybe we should rethink this. Regardless, this gentleman made my day with his good-natured attitude.
The gentleman says, "Young lady, I have noticed that everyone that comes out that door doesn't look happy - what happens in there?" I replied, "It's a biochemistry building - we're all grad students." His wife interjects, "So - a lot of work."
The gentleman comes back, "But why does NO one look happy?" Instead of all the jaded, cynical quips I could give about grad school, I decide to go with, "Well, we're all inside working on this beautiful day." And he chuckles, and says something like, "Well, when you're retired like us..."
It says something, though, when someone notices that EVERYONE that comes out of the biochemistry building looks unhappy. Maybe we should rethink this. Regardless, this gentleman made my day with his good-natured attitude.
7.13.2011
Vaccination conundrum
Saw this come up on my reader today:
Vaccine requirement
It talks about pediatricians who are turning away patients who are not vaccinated. To be honest, I don't know how I feel about this.
On the one hand, I am thrilled that someone is standing up to the people who think vaccines are more dangerous than, say...whooping cough (perhaps my favorite example because I work on its cousin). On the other hand, I'm a little taken aback by the idea of turning patients away.
I understand the reasoning behind it - they don't want to jeopardize the health of the other patients coming in by mixing vaccinated children, children who may carry vaccine-preventable diseases because their parents thought they didn't need to vaccinate their own children, and children with other problems who are medically unable to receive vaccines. If someone who was not vaccinated passes, say whooping cough, to even the aunt or big brother of an infant who has not yet received the full vaccine course, that infant can easily become infected and die. All because they were in the same waiting room as someone who had whooping cough. Read about strategies to prevent this.
I use whooping cough as an example, not only because I work on it, but also because, in older patients, like the aunt I described earlier, it would present more like a cold or flu. Give it to an infant, and suddenly it actually looks like whooping cough, and the baby basically coughs itself to death. I attended a Bordetella conference (whooping cough is caused by Bordetella pertussis or Bordetella parapertussis) last year, and at least two or three presenters forced us to listen to a baby whooping - it may be one of the saddest sounds ever recorded. Whooping cough is also a re-emerging pathogen, which means it's coming back, partly because newer vaccines with even fewer small side effects probably need more boosters to keep immunity high, partly because a closely related bacteria can also cause whooping cough symptoms and doesn't respond as well to the vaccine, and probably partly because many people have stopped vaccinating their children.
However, I am not convinced that blocking unvaccinated children from being their patients will solve the problem they claim. The other patients of these doctors could run into unvaccinated children in daycare, at the mall, or on the playground. But, if their point is to bring awareness and force some kind of consequence on people who choose not to vaccinate their children, then I guess I say "well-played."
Vaccine requirement
It talks about pediatricians who are turning away patients who are not vaccinated. To be honest, I don't know how I feel about this.
On the one hand, I am thrilled that someone is standing up to the people who think vaccines are more dangerous than, say...whooping cough (perhaps my favorite example because I work on its cousin). On the other hand, I'm a little taken aback by the idea of turning patients away.
I understand the reasoning behind it - they don't want to jeopardize the health of the other patients coming in by mixing vaccinated children, children who may carry vaccine-preventable diseases because their parents thought they didn't need to vaccinate their own children, and children with other problems who are medically unable to receive vaccines. If someone who was not vaccinated passes, say whooping cough, to even the aunt or big brother of an infant who has not yet received the full vaccine course, that infant can easily become infected and die. All because they were in the same waiting room as someone who had whooping cough. Read about strategies to prevent this.
I use whooping cough as an example, not only because I work on it, but also because, in older patients, like the aunt I described earlier, it would present more like a cold or flu. Give it to an infant, and suddenly it actually looks like whooping cough, and the baby basically coughs itself to death. I attended a Bordetella conference (whooping cough is caused by Bordetella pertussis or Bordetella parapertussis) last year, and at least two or three presenters forced us to listen to a baby whooping - it may be one of the saddest sounds ever recorded. Whooping cough is also a re-emerging pathogen, which means it's coming back, partly because newer vaccines with even fewer small side effects probably need more boosters to keep immunity high, partly because a closely related bacteria can also cause whooping cough symptoms and doesn't respond as well to the vaccine, and probably partly because many people have stopped vaccinating their children.
However, I am not convinced that blocking unvaccinated children from being their patients will solve the problem they claim. The other patients of these doctors could run into unvaccinated children in daycare, at the mall, or on the playground. But, if their point is to bring awareness and force some kind of consequence on people who choose not to vaccinate their children, then I guess I say "well-played."
7.12.2011
On the Road to Recovery
What a crazy weekend. The only time I didn't have to keep running (sometimes actually running, like to get the garlands for the milni, and to keep the boys away from the shoes we had to steal) was after the mendhi, but that's because no one could use their hands, so we couldn't do anything, which in and of itself was entertaining. It was a pretty great weekend, craziness and all. I'm pretty sure I had fun...looking back. At the time I was a little too busy to notice.
Of course, now that I'm back, I'm heading straight back into the science fray. Here's to hoping some of my experiments start working! It would be nice to be able to get a few things out of the way, so I feel better about getting some writing done, and starting to look for a postdoc and/or job.
I think a reasonable set of goals for while my advisor is gone for three weeks is:
1. Having a draft of the second paper (minus the onery experiment) ready to go.
2. Making a list of people who I am ready to send emails to, and for which I might need recommendations.
3. Be as close to done with these western blots as possible.
4. Send at least one sample to mass spec.
I'm not going to kid myself that I will have made the mutant that has eluded me for years. Some of the time that my advisor is gone, my boyfriend will also be gone, so we can pretend that means I'll get more work done, when in fact, it probably means less.
Of course, now that I'm back, I'm heading straight back into the science fray. Here's to hoping some of my experiments start working! It would be nice to be able to get a few things out of the way, so I feel better about getting some writing done, and starting to look for a postdoc and/or job.
I think a reasonable set of goals for while my advisor is gone for three weeks is:
1. Having a draft of the second paper (minus the onery experiment) ready to go.
2. Making a list of people who I am ready to send emails to, and for which I might need recommendations.
3. Be as close to done with these western blots as possible.
4. Send at least one sample to mass spec.
I'm not going to kid myself that I will have made the mutant that has eluded me for years. Some of the time that my advisor is gone, my boyfriend will also be gone, so we can pretend that means I'll get more work done, when in fact, it probably means less.
7.06.2011
Hittin' the road, Jack.
The last major trip of my summer (that I know of) starts tomorrow. I'm maid 0f honor in my friend's wedding this weekend. She's American and he's Indian, and there will be both an American and an Indian ceremony in the same day. It will be a whole lot of crazy, but it will be a good break from lab and thinking about work. Hopefully I can come back relaxed and re-energized to work. Also, hopefully in the meantime my cells rethink their bad behavior and come to their senses so that I can graduate eventually.
Also, my advisor got back from her trip to do a pilot screen. Sounds like I get to do some assays while she's on vacation to earn my pay from the grant that's giving me my stipend. I feel so...used. Oh, well.
Also, my advisor got back from her trip to do a pilot screen. Sounds like I get to do some assays while she's on vacation to earn my pay from the grant that's giving me my stipend. I feel so...used. Oh, well.
7.04.2011
Happy 4th of July, everyone!
I am celebrating by taking advantage of something cited in a PhD comic from last year:
http://www.phdcomics.com/comics/archive.php?comicid=1338
Free parking on campus.
Yep--I'm in lab for the bulk of the day - of course, some of what I'm doing didn't work, but "that's what puts the re- in research," right? Then it's home to do laundry, maybe take the dog to the park, grill, and watch some fireworks. Busy busy busy.
I am celebrating by taking advantage of something cited in a PhD comic from last year:
http://www.phdcomics.com/comics/archive.php?comicid=1338
Free parking on campus.
Yep--I'm in lab for the bulk of the day - of course, some of what I'm doing didn't work, but "that's what puts the re- in research," right? Then it's home to do laundry, maybe take the dog to the park, grill, and watch some fireworks. Busy busy busy.
7.03.2011
Everything but.
I am apparently doing everything in my power not to actually work on my dissertation. Today, I cleaned the entire apartment, went to lab briefly, made dinner, brownies, took a nap, talked to my parents, gave my dog a bath, and only just now starting to do some reading I guess. Oops. It's just hard motivation when it feels like there is so much to do. Maybe it will help to break it down into smaller goals...I will have to think about that.
7.02.2011
The future is scary.
Had a great dinner/venting session with a classmate of mine tonight. She and I even rotated in the same lab our first year together. She's had a rough go of it with her advisor lately, but has finally set a date for her defense. Now I'm feeling even further behind. When will I be ready? I don't know if I will ever feel ready.
7.01.2011
Need to start thinking about buckling down...
Inspired by the blog of a girl I used to work with in undergrad, I think a list of goals sounds like a good plan. I think the goal of this will be by the start of the school year...
Lab-wise:
1. Make the mutant that has been eluding me for years, or at least come up with some other ways to get it made. It's the last piece of my second paper.
2. Mass-spec some of the proteins we'd talked about doing since forever ago.
3. Continue to identify members of my regulon (this may never truly be complete).
4. Organize my strains, primers, plasmids and make digital spreadsheets of all of them.
5. Start getting protocols ready to leave behind.
6. (and most boring)- make Tables of Contents for all my lab notebooks - something I'm going to seriously regret not doing as I went- I am about to start Notebook #13)
Writing-wise:
1. Get the first paper resubmitted. Basically, bug my advisor until it happens.
2. Get a draft of the second paper done (leaving appropriate holes for when that mutant gets made).
3. Have at least a draft of every chapter of my thesis (This is probably impossible. I could be ok with a draft of my intro chapter and my two main papers, a really rough draft of the third main paper, and outlines of all my appendices).
4. Set a date for my defense. Also going to be tricky to do w/ no advisor around...
Post-doc exploration:
1. Make a short list of people I'm interested in contacting. Read info about them and figure out how I might fit in their research.
2. Update my CV, and start drafting "cover emails."
3. This is the tricky part, because my advisor is gone for three weeks starting the end of July, but decide who will write my recommendation letters, and get their ok to be my references.
Life-wise
1. Survive being maid-of-honor in this crazy wedding next weekend.
2. Keep walking/running, and try not to revert to crazy studying snacking with no exercise. I don't need to gain any thesis weight...
3. Set aside some money for a small trip after my defense.
4. Just try to keep some balance between crazy graduating and sanity.
Lab-wise:
1. Make the mutant that has been eluding me for years, or at least come up with some other ways to get it made. It's the last piece of my second paper.
2. Mass-spec some of the proteins we'd talked about doing since forever ago.
3. Continue to identify members of my regulon (this may never truly be complete).
4. Organize my strains, primers, plasmids and make digital spreadsheets of all of them.
5. Start getting protocols ready to leave behind.
6. (and most boring)- make Tables of Contents for all my lab notebooks - something I'm going to seriously regret not doing as I went- I am about to start Notebook #13)
Writing-wise:
1. Get the first paper resubmitted. Basically, bug my advisor until it happens.
2. Get a draft of the second paper done (leaving appropriate holes for when that mutant gets made).
3. Have at least a draft of every chapter of my thesis (This is probably impossible. I could be ok with a draft of my intro chapter and my two main papers, a really rough draft of the third main paper, and outlines of all my appendices).
4. Set a date for my defense. Also going to be tricky to do w/ no advisor around...
Post-doc exploration:
1. Make a short list of people I'm interested in contacting. Read info about them and figure out how I might fit in their research.
2. Update my CV, and start drafting "cover emails."
3. This is the tricky part, because my advisor is gone for three weeks starting the end of July, but decide who will write my recommendation letters, and get their ok to be my references.
Life-wise
1. Survive being maid-of-honor in this crazy wedding next weekend.
2. Keep walking/running, and try not to revert to crazy studying snacking with no exercise. I don't need to gain any thesis weight...
3. Set aside some money for a small trip after my defense.
4. Just try to keep some balance between crazy graduating and sanity.
6.28.2011
It was kind of a rough weekend, but I'm getting through.
First things first: making a slideshow for my friend's wedding is a GREAT distraction from what I really should be doing, which is writing. Oops. But it is definitely fun to go through old pictures and find little themes within them...if only that were a paying job. But then I suppose I wouldn't enjoy it as much if it were actually my job.
Second, why can't universities figure out climate control?? The lab is miserable and humid and warm, but one of the labs downstairs is freezing. But it makes it terrible for trying to do experiments, especially since I'm allergic to mold, and humidity = bad sinuses + mold = worse sinuses. Try having to put on a lab coat and work w/ radioactivity when it's miserably warm in the lab. The thermostat on the wall says 77. Bleh. 80 degrees is the same temperature as most of my experiments. Really annoying.
I think I might try to do mini-reviews of papers on here. Unfortunately, currently that means I might review papers only relevant to my research, but hopefully I will be able to branch out. More on that later...first I just need to survive and not melt in lab.
First things first: making a slideshow for my friend's wedding is a GREAT distraction from what I really should be doing, which is writing. Oops. But it is definitely fun to go through old pictures and find little themes within them...if only that were a paying job. But then I suppose I wouldn't enjoy it as much if it were actually my job.
Second, why can't universities figure out climate control?? The lab is miserable and humid and warm, but one of the labs downstairs is freezing. But it makes it terrible for trying to do experiments, especially since I'm allergic to mold, and humidity = bad sinuses + mold = worse sinuses. Try having to put on a lab coat and work w/ radioactivity when it's miserably warm in the lab. The thermostat on the wall says 77. Bleh. 80 degrees is the same temperature as most of my experiments. Really annoying.
I think I might try to do mini-reviews of papers on here. Unfortunately, currently that means I might review papers only relevant to my research, but hopefully I will be able to branch out. More on that later...first I just need to survive and not melt in lab.
6.25.2011
Can grad students get maid service as part of their stipend?
Weekends always seem like such good times to get a lot of writing done; I'm spending less time in lab, so I can spend more time at the computer, right? I always forget that I also have an apartment, a boyfriend, and a dog that all need attention, too. If only we got maid service as part of our stipend! They pay us to not have other jobs so we can focus on our research, but if they really wanted us to focus they would take away a few more distractions, such as needing to clean.
6.24.2011
Pondering productive procrastination
This has been one of those weeks where I work hard trying to get an experiment to work, and nothing really happens. I have a lot of good information that is just a little more confusing than it was before, presents more questions than I started with, and begs for more control-like experiments to figure out why something looks the way it does. Is it more important to figure out the answer, which could take awhile, or is your time better spent on other things? How do you decide? Part of me really wants to know, because it could be something important to the project. Another part of me knows that I will never really figure it out; it may be nearly impossible, or worse, may be an artifact of the way the protein was prepared.
It's always a hard decision to go to your advisor and ask for help interpreting results. On the one hand, she's more experienced than me in some areas and adds a different perspective. On the other hand, this technique is done more by my collaborators, so talking to them first would help. If only things weren't complicated further by the advisor leaving next week to do some experiments in Boston. I think I will try for one more week on my own before begging for help.
At least I have picked slowly at parts of my papers this week, including getting a draft of a resubmission back to my advisor, and making some figures for the next paper (which, by the way, only needs one more mutant to be made- a mutant I've been trying to make for three years now...). I've even added maybe a paragraph to the intro chapter of my thesis, and written the methods section for a paper I'm second author on with one of my collaborators in another lab. Hopefully this weekend will bring on more sections of my thesis.
I find that working on my papers and my dissertation is a great way to procrastinate what I REALLY should be doing - which is looking for a postdoc. The whole process overwhelms me, though. I think I have an idea of the general geographic location I want to be, but what I want to study, who I want to work for, and what I need to do to get ahead are beyond me. It doesn't help that I feel less confident in what I want my ultimate career to be than before I started grad school. I realize that I need to just start picking people and sending them emails, but I guess I'm just scared out of my mind about making the wrong decision.
It's always a hard decision to go to your advisor and ask for help interpreting results. On the one hand, she's more experienced than me in some areas and adds a different perspective. On the other hand, this technique is done more by my collaborators, so talking to them first would help. If only things weren't complicated further by the advisor leaving next week to do some experiments in Boston. I think I will try for one more week on my own before begging for help.
At least I have picked slowly at parts of my papers this week, including getting a draft of a resubmission back to my advisor, and making some figures for the next paper (which, by the way, only needs one more mutant to be made- a mutant I've been trying to make for three years now...). I've even added maybe a paragraph to the intro chapter of my thesis, and written the methods section for a paper I'm second author on with one of my collaborators in another lab. Hopefully this weekend will bring on more sections of my thesis.
I find that working on my papers and my dissertation is a great way to procrastinate what I REALLY should be doing - which is looking for a postdoc. The whole process overwhelms me, though. I think I have an idea of the general geographic location I want to be, but what I want to study, who I want to work for, and what I need to do to get ahead are beyond me. It doesn't help that I feel less confident in what I want my ultimate career to be than before I started grad school. I realize that I need to just start picking people and sending them emails, but I guess I'm just scared out of my mind about making the wrong decision.
6.23.2011
Getting Started.
As I start to finish up my PhD, I have decided to record a little bit about the everyday ups and downs of trying to just get everything done, and figure out exactly what to do next with my life. My hope is that this will resonate with a few, but mostly serve to get a little of my crazy out of my system, as well as hold me a little more accountable for all the bits and pieces I need to accomplish along the way. It will at least get me to write a little about something every once in awhile, even if this isn't exactly my dissertation...
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