Friday, December 28, 2007

Followup on Leopard upgrade.

Oh, how I hate upgrades. The funny thing about upgrades is, they make everything stop working for a while.

As Seinfeld would say, What's UP with THAT????

Yes, I have to upgrade from CS2 to CS3. I knew I would need to do this, and I didn't buy the upgrade ahead of time for a variety of reasons, none of which seem to make any sense now.

So what are my choices?

a) order it online and wait for 3.2 GB download.
I don't think so! I'm sure my connection would die in the middle!

b) order it online and wait for ... days? for a $400 box that I hope doesn't get lost in the mail (or stolen).
I don't think so!

c) attempt to enter a store, in a mall, during the mad post-christmas shopping rush. Aaaack!
Not my idea of fun!

d) wait for the campus computer store to re-open when the semester starts.
I can't wait that long!

I don't like these choices!!

Yes, I lost all my printer settings and haven't gotten around to putting them back in.

Yes, most work is stopped until I get CS3 and printing fixed.

No, I can't afford to be not working.

Yes, I will be fixing these things over the weekend.

Yes, I am annoyed about this.

No, it's not really worth the one or two cute features in Leopard that I like, or the very slight increase in speed (irrelevant when considered in terms of time lost fixing these other problems)!

No, I'm NOT happy with Apple right now!!

I love how they make fun of Vista on their commercials, and then their own upgrade is not exactly a giant leap into the amazing future. Grrrr!

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Life vs. work

Well, life marches on. Another friendship peters out, as we grow our separate ways.

This is one of those friends from grad school who went to industry.

She has a love/hate relationship with her job (better than the hate/hate she felt in grad school), is looking to get a new job and move away, and puts almost all of her spare time into competitive sports.

I've been kind of sad the last couple of days about being forced to face that we're just in different places with our lives, but today I am trying not to worry about it. As with most of my friends who are far away, we'll always be like family (in a good way!).

I'm trying not to look at it in the context of having had this happen already with all my other good friends from grad school, and amazingly, right this second I'm not bothered that I don't have any new close friends to fill the void while I'm still stuck here.


Actually I am in an oddly good mood, mostly because it's hard for me to be depressed when things are progressing at work.

Yes, the data monster was fed this week, so I am happy!!!

I love the part where I have so many ideas for what to do next that I get to sit and bask in the decision, where all the experiments I can think of will give me some new insight, it's just a question of which one to do first. What to do, what to do...

And I am torn about how to spend my last few precious days of 'vacation' - finish cleaning the house? Plan experiments in anticipation of the new semester? Watch movies (I want to see the new one with Will Smith) before everyone at work and the associated guilt and stress comes back in full force?


This is going to be one of those years where a New Year's celebration doesn't fit with how things feel. It feels wrong to start a new year in the middle of winter. It's too early to me, to get into the spirit of 'new beginning' and making new resolutions- I'm still struggling with the ones from the last few years! Maybe I'll celebrate Spring instead, when we get there...?

Still, this year sucked, so I am feeling some relief, however superstitious, about the whole switch to '08.

Even numbers, an extra day in February, maybe a new (woman?) President?!

So yes, I'm hoping against all logic that next year will be better.

Mostly I'm impressed that I'm still capable of feeling hope!

The human spirit... not a rational thing. I was talking to a friend the other day about the psychology of winning/losing, which I found very interesting. He said it has been shown that people hate winning all the time (boring) or losing all the time (depressing). Apparently, to keep people motivated and happy, you have to have some of both.

I think this is something The Powers That Be should take into account.

Soon. Please. Thanks.

I guess for me doing experiments is enough of a gamble, you make your hypothesis and then you roll the dice.

Contrary to some models of motivating the worker bees, I don't agree that we need to keep our personal lives in a state of arrested development while we do it.

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Monday, December 24, 2007

Holiday procrastination.

Not much going on this week. Stupid holiday parties with greasy food and lots of alcohol. Yum.

Mostly I've been biting my tongue, trying not to snap at people asking how the job search is going. What is it about holiday parties that gives otherwise shy people the courage to ask incredibly insensitive questions?

I finally lost it the other day at a friend who is visiting from out of town. Hint: I'm trying not to complain so much (at least in real life), so if I'm not talking about it, I have nothing good to say!

(If you're reading this, my apologies.)

Meanwhile, I'm in holiday procrastination mode.

I don't mean I'm procrastinating about the holiday itself. I did all my shopping and delivered most of the gifts already. (I strongly suspect they have all been opened even though it's not actually Christmas yet.)

No, I mean real procrastination. I have work to do, I really do.

The work I really want to do, I can't do until January.

The work I don't want to do... seems less appealing even than cleaning my house.

So I am prioritizing (aka procrastinating about by writing blogs) how I am going to be cleaning my house. In theory, this will make me feel better about doing the work I don't want to do, because I really hate cleaning.

Do I tackle the grout in the bathroom? Or the kitchen floor? Decisions, decisions.

I did the dishes. Then I dug out my desk from a giant pile that got moved there the last few times we had someone drop by for dinner. Mail (bills, coupons that will expire before we think about using them) and journal articles tend to accumulate on the kitchen table. Actually there are journal articles everywhere. I'm trying to file them, I swear.

Dear Mac,

I love the new Preview that came with Leopard. I will try to read papers this way instead of printing them out. Thank you for saving the trees I have been killing.




Mostly I love this place that we've been renting. But the other day I was noticing that I have a curling iron that I haven't been able to use in years, because we don't have any electrical plugs in the bathroom. And I thought, "Should I get rid of that?"

Mostly the thing that has been bugging me about the lack of job... is that the last 2+ years I keep thinking we might be moving, because either my funding will run out, or I will get promoted. It's a weird tightrope to live on. I think you're supposed to walk across it in a relatively short amount of time, but I'm literally camped there. I have a tent and everything.

So we might be moving, but we don't know when or where. So then I think, "Should I get rid of these old clothes? Should I get a suit for the mythical future interviews?"

And I think about getting rid of most of the things I own, because I figure hey, that helps if we move (keeps the cost down) OR if we're homeless (nowhere to put them anyway). Except for the old clothes. I'm going to need to those to keep warm in layers when I'm sleeping on a sewer grate.

The thing that bugs me the most is that we really are worse off than our parents.

I realized that somewhere deep down, I thought I would have, you know, an electrical plug in my bathroom by now. Not that I need to or want to curl my hair on a daily basis, I just wish I had the option to, once in a while. You know, when I have to get dressed up for lab Christmas parties, put on a polite face, and bite my tongue. At least my hair would look good, even if I have no career progress to report.

Okay moldy grout, here I come.

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Sunday, December 23, 2007

Go, go, go.

Someone wrote a comment about whether it's okay to rest on one's laurels or take a break or if it's got to be 'go go go' all the time.

Dear lazy old PIs who want to rest because you've been working hard all your lives,

Take a week off a couple times a year if you need to. You deserve it.

Just don't hang on to a job you're not actually doing.

Especially when there aren't enough jobs for younger, more energetic people who have tons of new ideas and no resources to test them.

Don't "rest on your laurels" by taking credit for what your younger colleagues are doing.

Especially don't do this by keeping them as slaves in your lab writing your grants, making slides for your talks, teaching your students, and generally everything else you're supposedly getting paid salary and grant funding to do.

Oh yeah, and if you're one of the ones taking a week off now and then, tell your lab slaves they deserve the same.

That's all.




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Thursday, December 20, 2007


These old guys need to retire.

There, I said it. I've said it before, and I'm sure I'll say it again.

Today I got behind one of these old bald guys in a BMW, driving under the speed limit to his reserved parking spot on campus.

I hate old guys who buy sports cars and then drive them under the speed limit in front of me when I need to get to work!

When I got to campus, I saw one group of three old white guys standing around talking on one side of the building.

When I was doing experiments, I was running around inside the building and saw another group of three old white guys standing around talking.

I wanted to yell at them, Are you actually getting anything done, you lazy bastards!!!

I wanted to tell them if they don't want to do any work, they should just go home and leave us alone instead of standing around gossiping and bragging and having a pissing contest, or whatever the hell it is they're doing.

Ok, there, I said it. Experiments will recommence now.

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On what to read.

Anonymous said...

ok, msphd,

here's a practical question for you or your readers.

i'm a grad student. i perform pubmed literature searches daily on the key words of my thesis project. most of my reading, then, is directly related to my thesis project. how do you find or decide which papers to read that are outside your narrow area of focus?

any advice is appreciated.

anon grad student wannabe reader

Dear Anonymous,

Thanks for this interesting question, since otherwise I would be tempted to rant today. I am in that kind of mood.

In the interest of being more interesting, here's my advice.

Read about things tangential to what you work on.

They can be tangential in the sense of, homologs of your protein or analogous appendages in other species.

They can be tangential to your technique. Let's say you work on a protein that has no known homologs, but it would be really helpful if somebody could find one. Read about homology searching algorithms. Read about structural biology, since there might be a structural homolog even if there's no a sequence homolog. Think about why there might not be one, evolutionarily speaking.

They can be tangential to your pathway. Let's say you work on why hair is curly (I'm making this up, I know nothing about how that works!). Maybe hair is curly due to changes in the stem cells at the root of the hair follicle, or due to hormonal changes, or genetics (?). Read about those things, even if it's just at the level of Scientific American reviews.

Read about neat new stuff, even if it's totally unrelated to what you do right now. I'm very excited about the possibility of having wireless laptop charging by development of new technology to transfer electricity through the air! Read about how astronauts adjust to low gravity. Give yourself permission to daydream a little on a daily basis!

Read about science that affects your daily life, like the science of food (nutrition, agriculture?) or about additives they put in shampoo or to remove wrinkles from your skin.

Read widely, and I promise you will have new ideas. If nothing else, it will help you decide what to make for dinner!

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Friday, December 14, 2007

Response to comment on last post- in defense of reading a lot.

Dear Anonymous,

In terms of getting a PhD whether you like reading or not, I think that we shouldn't abuse students who realize halfway through that they don't like reading. I'm in favor of terminal master's degrees (TMS) as per the discussion over on FSP's post about that. I think it's better for people to leave at that point than to try to finish "just because", or even worse, go and do a postdoc because they can't figure out what else to do with their lives.

But, I do think that a certain amount of reading (and of course, writing!) should be a requirement for a PhD.

So maybe if you don't like reading, you shouldn't have gotten a PhD in the sense that it was not the best use of your talents?

Did you think about quitting? How did you end up finishing? Do you mind telling us (however vaguely), what you do now?

For me, getting a PhD was not easy. In fact, it would have been easier to quit (and justify quitting) than to finish.

So I wouldn't give back my PhD, either, because I know I earned it.

Whether I would do it all over again, if I had the chance, is a different question.

So I'm curious about what got you through? In fact, I generally invite comments, for the benefit of our grad & younger student readers, on that topic.

But I digress. To me, reading papers is not so much about minutiae.

I think a lot more experiments work when you read a lot and plan carefully based on what's already been done. That might sound hopeless trite, but bear with me.

Even when no one has ever done what you're setting out to do, there are always common features to be found, and those things can make or break your experiments.

I can see how those details would be boring to some, but I really like having experiments work (as you say you do). So details of that sort matter a lot to me. To me, one of the worst feelings in the world is when you find out later that someone else got your difficult experiment to work using some little trick you didn't know about. I HATE that.

Reading a lot helps me avoid getting into situations where I have to feel like that! It's that same feeling like when you leave your wallet in the backseat of the taxi cab. ARGH!

Today I was thinking about how a couple of people in my lab missed something kind of critical because of just that sort of mistake- they didn't pay attention to common features and they didn't do enough reading.

It's not my project, so who's to say I wouldn't have also missed all the clues, too. But it's kind of sad, because in retrospect, it was all sitting there in pubmed if they had just bothered to read it.

But you know, you can only do so much. And everyone handles the 'down time' differently. I think that's as much about personality as anything else. I am always in a better mood when my experiments are working!

Sometimes reading is the only thing to get me out of an experimental rut- and actually in this case, it did. The only reason my experiments are working so well lately is because of a paper I read that gave me an idea for something to do, and how to do it.

I like ideas. But I like them even better when I can show why they're right.

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Thursday, December 13, 2007

A maybe yay.

I think my experiments are finally back on track. I'm afraid to say it out loud though, because I am a little superstitious about the mysterious part between adding the reagents and getting the result.

So I am glad because I got some data today. But I am also tired, almost too tired to muster a 'yay!'

Tomorrow I will hope to keep building momentum. Last night I actually went home and read papers (while watching Project Runway) for the first time in a while. And I didn't mind.

I used to read journal articles almost every night. But lately I've been running around during the day a lot and so annoyed in general that I couldn't work before bed, or risk not being able to sleep for anger or anxiety.

But I am hoping things are on the upswing. I like the part where I get to read papers and think about my latest results.

I especially like it when I can perform the reaction:

idea + reagents = experiment ----> results.

Keeping in mind that all steps of this reaction are reversible, and it only yields product in the presence of large doses of hard work.

And here I add a letter of the sort profgrrrrl likes to write:

Oh, benchwork. Sometimes you are a soothing, meditative activity that doesn't feel like work at all. And sometimes you are a ball and chain.

I love you benchwork, but I am ready for our relationship to progress to a new level. Let's try to get there together. Sooner would be good. Is soon good for you?

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Thursday, December 06, 2007

On switching fields.

On my last post, someone commented that they really can't relate to my statement about how money matters more than ideas, but proposed that it could be field-dependent.

I think there are a lot of differences among different sub-fields of science. I find it odd that no one seems to care if other fields are unfair or corrupt, so long as their own field seems okay.

This person also suggested that I should consider switching fields.

I have. It's a little more complicated than it sounds. There are some times in your career when it will make sense to switch fields, or migrate, or straddle multiple fields. There are other times when it is virtually impossible.

Let's say you did your PhD in one or more fields, and now you're debating about what to do for your postdoc (this is geared toward what I think is my demographic of readers- mostly PhD students and early postdocs).

It's perhaps a little-known fact that NIH postdoctoral fellowships are preferentially awarded to people who switch fields- or at least appear to switch fields. (Note that this is not generally the case for other funding sources or non-postdoc-fellowship types of grants.)

I can state for the record that I met someone who served on the review committee and he confirmed for me that this is true, and that it is an unusual feature of the postdoc fellowship funding level. The belief system of this review committee is based on two main assumptions:

1) Switching geographical location is good for scientific training/career experience.
2) Switching scientific field is good for scientific training/science in general.

However, it is also very beneficial to have preliminary data for even a postdoctoral fellowship application.

There are a few ways to get this.

1. Bring something with you from your PhD. This only works if you stay in the same field or if your PhD advisor let you go off on a tangent at the end of your thesis work. I think this scenario is probably rare, but I'm sure it happens sometimes.

2. Use data your postdoc PI had lying around, for example from their R01. Think you can't use the exact same data in two different grants reviewed by different committees at NIH? Why would you think that? I know of multiple examples where the PI offered/insisted and the postdoc agreed. In none of those cases did anyone ever get caught for plagiarism or simultaneous submission.

3. Work hard and fast your first few months in your postdoc lab, and then apply. If you do this, there are three ways to get enough preliminary data to get funded:

a) Join a good lab where they will train you in their techniques and help you get up and running

b) Be a genius at the bench and work wicked fast (not me)

c) Do something related to your PhD experience, because you can do this quickly thanks to all those years of training.

d) Some combination thereof.

All of this sounds great, very simple when you break it down like this into pieces.

Now here's where it gets interesting. Let's say you get the money. Then what do you do?

1. Work on what you proposed.

2. Work on something other than you proposed.

For both of these scenarios you could say the following:

If it a) has something to do with what your current lab does, you're probably in good shape. You can rely on their existing reagents and expertise, and your advisor will happily supplement anything else you need because it overlaps significantly with his/her R01s.

If it b) has very little to do with what your current lab does, congratulations.

You're now straddling fields, whether you meant to or not. You may or may not get as much support from your advisor as the postdocs in your lab who work on sub-aims of the lab R01s. You may or may not have the resources you need. You will probably have to make and/or buy new reagents and you will probably have to hard time paying for them. It will take you longer.

The good news is, you might go outside your main lab and find other mentors in other labs. These contacts should be useful to help you get a job later, especially if you want to migrate over to this other field.

The bad news is, your advisor most likely will not understand what you're working on, and more importantly, he/she won't care very much, because you're going to take it with you when you go.

So now you're like a hairdresser renting out a chair in somebody else's shop. Everyone knows that's not a permanent arrangement, so they don't have to be nice to you, and in fact might be deliberately not nice to you, in an effort to hurry you out.

But I'm going off on a tangent.

Now let's say you're farther along in your postdoc and you've been straddling, as a tenant-hairdresser, for a while now.

You'd like to switch fields entirely but you can't easily do that, because your advisor is not an expert in your field of interest (and maybe people in that field have never even heard of him/her).

So although you've done work in this new field, it's hard to make the connections you need since you'd have to pay to attend meetings out of your own money, and do your own PR (since your advisor isn't do it for you). In order to get a job, you also have to publish in this new field, which again is hard since you and your advisor are unknown in this area. Your collaborators try to help, but it's not enough. You've even thought about switching to join your collaborator's lab, but for various reasons that didn't seem like it would work out.

And you're too expensive at this point for anyone to want to hire as a postdoc in your field of interest (and frankly too tired).

You have a blog where you occasionally write about these things, where well-meaning but clueless people occasionally comment with suggestions as if you haven't thought at all about how you're living your life.

So, to sum up: if you're going to switch fields for your postdoc, beware. One of my friends took the easy way out. She wrote her fellowships on a project unrelated to her thesis work, got the money, and then she didn't do what she proposed. She went back and worked on a followup to her thesis project, and got a faculty position BY STAYING IN THE SAME FIELD.

Newsflash: search committees are not impressed when you switch fields, unless you become a star in the new one. Oh and you better do it ultra-fast.

Even worse, if you're straddling fields, departments don't want you because they don't know where to put you. There's a lot of lip service about 'interdisciplinary' and 'cross-departmental partnerships' and yada yada, but in reality most departments are still very old-fashioned and provincial, and they want candidates who are that way, too.

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Monday, December 03, 2007

More responses to thoughtful comments.


Thanks for the correction, you're right.


I appreciate your point about demographics shifting, and I guess I still hope that might help change things. Who knows? In a few more years maybe the face of 'scientist' will be a woman, the way most of us still conjure a picture of a woman when we hear the word 'nurse.' It's not necessarily bad that we have these associations..... unless you're one of the minority.

Your assumptions that I don't understand what PIs are doing when they're protecting their own research program, however, are insulting.

Believe me when I tell you I've seen enough outright manipulation of projects and people to be well aware of what PIs have in mind when they're ignoring one person, pushing another, burying data, rushing papers, and all the other wonderful things people do when their money and ego are on the line.

I've seen, I'd like to think by now, it all.

While some grad students and postdocs might be able to persist in blissful ignorance, I have not had that luxury. I'm cursed with being overly observant... and always being in the wrong place at the wrong time.

I just hope that I won't be tempted to do half the shit I've seen PIs do, out of sheer desperation or selfishness.

I do appreciate your point of view that being non-anonymous would somehow help me and/or the system, but I'd argue that on balance, I still piss off more people than I please.

Or maybe the pissed-off people are just more vocal/memorable.

Either way, the experience of blogging has taught me that I probably wouldn't like being a celebrity. I can't imagine having people watching my every move and picking on everything I say.

Luckily, anonymity affords me the opportunity to pick fights just for the sake of argument, which I actually try to avoid doing in real life. Arguing in real-time makes me tired. And I mostly find it boring. If I can't convince you, okay. At least with writing, I can say my piece, and you can choose to read it or not. Putting it out there is usually enough for me.

And, um, contrary to your suggestion, I'm not strong enough to take on the establishment and win. If I were, I would have a job by now. I mean, are you kidding? You're kidding, right?

John Q. Jackass hasn't gotten his head chopped off because he doesn't stick his neck out. That's why he has a job and I don't. Just because I don't agree with it doesn't mean I'm not aware of how the system works.

I've thought about ditching this blog entirely and/or starting one under my own name where I would discuss, um, science. My science.

I guess the main reason I haven't is fear. Fear of
a) looking less professional through vanity publishing
b) pissing people off inadvertently.

Having this blog has taught me one thing, in case I had actually forgotten: you never know what's going to piss people off. You just really never know.


You're right, and I hadn't seen the Engineering Science blog, either.

I know what you mean about these ridiculous blanket statements about cutting or adding money to the NIH budget, as if the money is being allocated fairly in the first place. It's a huge problem, and I don't pretend to understand how much things at that level really cost, but I see so much waste on a daily basis that I can only begin to imagine what I would do differently if I were in charge.

Now that would be an interesting job.


Your point about "if you can afford to do the research then you should be able to afford to pay to publish it" is exactly my point.

Research is based so much on money and quantity now that ideas and quality are almost irrelevant.

But apparently the same could be said for comments like yours.

Sunday, December 02, 2007

Being a good citizen.

As pointed out by an alert reader, drugmonkey wants to keep talking about this point on a previous post about how/whether we can change the way science in the US is currently broken. Oops, I mean, whether we should have a say in fixing it.

One of the points raised was regarding this NIH RFI we discussed a while back.

I just want to point out again that when the NIH puts out an RFI, it's not advertised to everyone. Grad students don't hear about it, and neither do most postdocs.

Most of the PIs I know can't keep up with their email to save their lives, much less forward these things along to their lab members. They might be getting awards for being great citizens, but nobody seems to notice or care that they aren't doing anything to train their lab members or invite them into the scientific community.

I think this is why NIH got so few responses, and why everyone's vote doesn't count equally. It's designed to solicit input from a limited audience for a reason.

I think the system works really well right now to squash input from the youngest members. They don't want us getting distracted from our assigned slave labor. If we stopped to look around, they'd be in big trouble.

No, the system works really well to ensure that most grad students and postdocs are dog-paddling just to keep their heads above water. They're not sitting around saying,

"Gee, how can I make the system better? What can I do?!"

They're just trying to survive. They don't have enough energy or time to do more than that.

And most people's reaction to hardship is not to say,

"Let's fix this for future generations!"

The most common trend in science right now is actually:

"Get me the fuck outta here! Where's the door?!"

So they will do whatever they have to do to get out. That usually means keeping your head down and your shoulder to the grindstone.

I saw the same thing in school. All schools have to be reviewed every few years to maintain their accreditation, and mine was no exception. But the way they handled it was classic politics in action. Those of us who had, ahem, shall we say suggestions, were carefully hidden away (read: prohibited from talking) when the reviewers were present. They didn't want a real review. They just wanted to pass the requirements.

NIH does the same thing, just like the mainstream media, and the Bush administration, and any large group with power that doesn't want the naysayers to... have their say.

The same thing happened with Nature's stealth attempt at having an open access journal of their own. I personally think they did this on purpose. They didn't advertise it, and then they used their paltry turnout as evidence that open access will undoubtedly fail.

Similarly, some of these open access journals are purportedly less political/stratified than the traditional money making machines of commercial scientific publishing. But all you have to do is look at the publications fees to see that's not exactly true. Sure, they say they'll waive it if you're broke, but that's not exactly fair, either, since it means the rich labs are overpaying to support the poor ones.

I've written about this a lot, but I'll say it again: everything in science in the US is a hierarchy right now. And maybe it always will be.

Case in point: I get certain readers because I've declared that I'm a postdoc, and that I'm female.

I also get certain types of comments because of that.

Sometimes PIs come on here and tell me I'm wrong and what could I possibly know. Sometimes they're actually encouraging, but just like in my real life, that's the exception rather than the rule.

I get a handful of female grad students asking for advice, and even - oh, heartwarmingly! - stopping back in to say things have gotten better for them.

And I get a fair number of would-be peers, mostly green, male postdocs who come from a different caste of lab wondering why I'm so stupid that I didn't join a lab with infinite money, like they did.

Newsflash: even rich labs occasionally go through dry spells!

I might be complaining about being poor now, but I'm well aware that I'm more equipped to deal with limited resources than any of these people whose solution to everything is "switch labs and join a rich one."

But hey, I try to deal with my problems by a) venting on my blog and b) taking the long view.

What doesn't break me or make me stronger makes for interesting blog fodder.

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