Sunday, March 30, 2008

Don't think so much.

This last week or so I've been trying to stay in Work Mode and out of Self-Aware Mode.

Work Mode has been going along just fine. I'm getting things done. I have very specific, task-oriented goals in mind.

Only problem is that a friend came into town this weekend whom I haven't seen in a while.

Inevitably the questions are all about where I am with my life.

Which I'm not too happy about.

So I am trying hard to stay out of Self-Aware Mode. I think I have to stay in this particular sewage pipe until I can ride it into the ocean. So there's not much point in thinking about how much it stinks.

But it's hard when I finally take the time to get caught up on reading my favorite grad student blogs, and they're all graduating.

Where am I? Wishing I were getting on with my life, instead of stuck in the same sewage pipe.

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Wednesday, March 26, 2008

The Salsa Dance of Progress.

Research: On good days it's two steps forward, one step back.

Sometimes for a whole year (or a few), it's one step forward, two steps back.

Kind of hard sometimes to see the wisdom of dancing, if that's the dance.

Or as a friend of mine puts it,

some days you're the dog.

some days you're the hydrant.

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Monday, March 24, 2008

Useful things you'll need to know for modern biological research.

A nervous student interested in grad school asked me to elaborate on this since I said most undergrad departments don't teach what you actually need to know to do modern biological research.

I have lots of coy ideas for this post. For example I considered writing simply:

If someone would give me a faculty position, I could just teach it.

But since other helpful commenters have written things like:

No department would ever hire the person who writes this blog

I guess you probably don't want to wait that long to hear what I think. It could be a while.


I think most funded biological research now is biomedical. That could be a generalization, but I think most biology that's not even slightly related to medicine is probably underfunded these days.

That said, let's assume the basis of modern biomedical research is molecular and chemical.

Currently, biomedical research includes computational, nanotech, physics, and mathematics of biology.

At least, that's the stuff that gets funded.

Once upon a time, a few decades ago, biology departments did a lot of genetics research. They still do, but maybe not as much. Now it's a lot of stem cells, drug delivery, and signal transduction.

So far as I can tell, lots of departments still teach phylogeny like it's the epitome of biology and the obvious place to start.

Well, it is and it isn't. I personally think you can skip it, or maybe do it later on rather than as an 'introductory' course. It doesn't frame anything, really, so it doesn't make sense to do it first.


They still teach a LOT of genetics, and that makes sense to me.

DO take at least one genetics class.

If you want to work with flies or yeast, or make knockout mice, take more genetics. Lots more.

Otherwise, stop there and make sure you got at least 1 good semester of organic chemistry.

I don't mean memorizing and spitting out, I mean DID. YOU. GET. IT.

Do you know the pKa's of the amino acids?

Do you know what a buffer buffers?

Why are some things soluble in water while others aren't? What should you do about it if you need something to dissolve and it doesn't?

How does PCR work?

How long does a PCR primer have to be to make it specifically bind a sequence of DNA?


Take statistics.

Take differential equations.

Take a nonlinear dynamics course if you can get into one. It's usually a pretty high level elective.

If you can't do that, read Sync by Stephen Strogatz.


Take some history of science. Did you read The Double Helix and The Dark Lady of DNA?

Have you read a biography of Marie Curie? There are several to choose from. How about Barbara McClintock?


Did you do optics in your physics class? Do you understand how microscopes work?

What about lasers?

Lots of modern equipment is based on lasers and fluorescent light. Do you understand where fluorescence comes from?

What's the one critical feature that lets us separately detect different colors of fluorescence dyes?

Do you know how modern DNA sequencing works (hint: it uses fluorescence)?


How's your computer science? Could you write a program to sort files for you if you knew the file name format? Do you know what symbols are generally frowned upon filenames, and why?


Do you know how to use PowerPoint? What about a spreadsheet program? What about Endnote?

Have you ever taken a writing course - of any kind?

Have you ever taken a public speaking course?

Have you ever taken a drawing course?


I'm not saying you have to know these things. I'm saying you should make it your business to learn these things.

I could make a much longer list, but I'm kind of tired. I spent the day on an experiment that didn't work.

Oh yeah, I forgot to mention that if you want to do biological research, you need to learn how to deal with failure on an almost daily basis.

I know, they don't teach THAT in college.

I learned it from my extracurriculars. Ever watched America's Best Dance Crew? You should, because dancers are used to getting criticism even on their best work, EVERY DAY. Musicians too. Sports are the same way, if you play semi-seriously, your coach will be on your ass to always be improving.

If you can handle that, and be your own coach, you'll do okay.

You have to learn how to pick yourself up and just keep bashing your head against the wall until you make it through.

Most people don't learn that until the end of grad school.

If you already know it going in, you'll probably wonder why everyone else is always complaining.

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Sunday, March 23, 2008

Writing matters.

Here are two parodies of the same imaginary story written up as abstracts for Cell/Science/Nature vs. A Specialty Journal. Which one would you send out for review?

Specialty Journal Version.

Crystal structure of gobbledegook bound to schmutz
Authors: Grad Student, Undergrad, PI.

The crystal structure of gobbledegook bound to schmutz in complex with peanut butter identifies a distinct mode of jabberwockying junk. Gobbledegook binds to schmutz via the conserved ACDC domain.

Cell/Science/Nature Version.

Molecular mechanism of junk recruitment by economic downturn
Authors: Postdoc, Grad Student, Actual PI, Famous PI who did nothing.

How junk is jabberwockied is a longstanding problem in biology. Here, we tested the hypothesis that junk is jabberwockied by economic downturn by examining the crystal structure of gobbledegook bound to schmutz. Surprisingly, the conserved ACDC domain is required for jabberwockying junk, revealing the molecular mechanism of economic downturn as a novel basis for junk recruitment to jabberwockying sites.

In terms of the actual scientific content, the same work written up different ways can have completely different chances, because most journals make their initial decision on whether to send a paper out for review using only the abstract and author list.

You're kidding yourself if you think that the writing, and who does it, is not important in determining where your papers get published, who ends up reading them, and how much they get out of it.

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Saturday, March 22, 2008

Comparisons of biologists vs. math, continued.

Anon 2:22,

Well yes and no. The paper might be only the tip of the iceberg in terms of the work.

The problem is that papers are still really the only currency we have, iceberg tip or not, we don't have much other proof that we did anything.


Although I consider myself at least as smart as most physicists and mathematicians I meet, I guess you are qualifying it by saying that physicists and mathematicians are 'smarter' than most biologists "on average"?

I would tend to disagree, but I've blogged at length in the past about the different kinds of intelligence/smarts, so I won't do it again here. Of course I'm too lazy to figure out which posts those were. One of these days I swear I'll go back through and tag them.

I guess I can see what you mean by physics requiring more raw brainpower.

If you're not good with your hands, if you have no aesthetic sense, you won't be good at biology.

Some people seem to think 'raw brainpower' measured in math is somehow more important, more valuable, or otherwise more useful in life.

It's not.

Raw brainpower isn't all that good at running pretty gels or observing differences in morphology. Raw brainpower is usually not such a great mentor or teacher, either.

If you want to be good at biology, you gotta have good hands, and you gotta have good eyes. So raw brainpower is part of the equation, but it's not the whole enchilada.

I think you can train most any muscle, including your brain, but only so much.

If you're totally uncoordinated and tend to knock over bunsen burners and set benches on fire (like a lab partner I had briefly in college), you'll tend to feel safer doing math. Only so much damage you can do with paper cuts and broken pencils!

I did not know that physics majors do better on the MCAT than biology majors. But honestly, it doesn't really surprise me. Most of the people I work with in biology now were not biology majors in college.

Modern biological research requires a very different background than the curriculum most college biology departments teach.

And by the way, to hell with the MCAT. Why do I care about anyone's scores on the MCAT? So far as I know, no one has done a study to show any correlation between MCAT scores and rate of obtaining faculty positions doing research.


As for (3), that really was not how your original comment read.

Your general implication, that most biology postdocs are idiots who are easily mislead, is pretty condescending. Maybe that's not how you think about it, but that's how you sound.

On the other hand, I do think that if biology did what physics does by limiting the number of slots, it might be better for everyone. But I don't see it happening. Just the opposite.

Did you see that Congress will discuss the possibility of increasing the number and salary for NSF graduate fellowships? The theory is that better students will have more incentive to stay in science if they get one of these.

I definitely think grad students should be paid more.

But I don't think we need more of them. Far from it. I'd rather have three great students, paid well enough that they don't need to worry about it, and have plenty of time to mentor them in my (future imaginary) lab, than 9 mediocre grad students and not enough time to help them all.

But hey, that's more than just raw brainpower talking.

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Thursday, March 20, 2008

Are most postdocs and grad students just glorified technicians?

CC said:

Math is a completely different situation, where advisors do their own research and mentor the research of others. In experimental sciences, where the advisor's job is almost entirely driving the research of others, the vast majority of grad students and even postdocs are glorified technicians. They contribute a bunch of figures and some methods and results text to the PI, but do not "write papers" in what I would consider a reasonable sense of the phrase. Only in the top 10 or so programs in the US, and their counterparts internationally, do even a majority really manage publications.


I can't say I would know. But here's what I think.

I've worked at places that are maybe in the top 20, maybe top 30, and at least one or two in the top 10.

So far as I know, most senior grad students were doing a significant portion, if not most of the writing, of their papers. Most postdocs were putting together their own manuscripts... or at least I thought they were?

Ever since my very first paper in grad school, I've been doing everything myself. My advisors have contributed edits only. Which I think is perfectly reasonable.

Having said that, though, my most recent manuscripts have gotten more edits, and more useful comments, from people who are not authors.

In fact, come to think of it, on my last few papers, the second/middle authors contributed a reagent, technical help, and/or maybe up to a paragraph of text.

None of these people made even one figure for the paper. The senior authors did even less than that.

But you wouldn't know that from looking at the author list.

So I think it's hard to know how anyone would have such a broad sampling of that kind of inside information as to be able to comment on 'the vast majority' of grad students or postdocs with regards to manuscript writing.

So far as I know, detailed documentation of actual contributions of individual authors is spotty at best (?).

It has only been recently that journals have started including specifics of author contributions at all in my field. Even now, it's not in all journals, and it's often optional or inaccurate.

Here's the kind of thing we put when it's required of us:

Professor X contributed helpful discussions of the results, and contributed to the writing and editing of the manuscript.

Here it is with the subtext revealed:

Professor X contributed (un)helpful discussions, and contributed (very little) to the writing and editing of (an earlier version) of the manuscript (and hasn't read it since, despite being given multiple drafts, junk food bribes, and a deadline).

And here's what I would have written if I were being completely honest about my advisor's contributions to my last few papers:

Professor X rewrote some of my sentences to make them run-ons. X made me use a title I hate, but the paper got in so I don't care anymore because I'm tired of fighting about it.

Professor Y did not contribute more than a few word changes, but is nevertheless an author since Y's grants funded part of the work.

Professor Z read an early draft of the paper and said it looked fine. Z is an author since the work was done in Z's lab space and we can't afford to piss him off.

What do you think, readers? Is CC right? Are math students so much more independent than we are? Is the vast majority just glorified technicians?

Or is this yet another myth being used as justification for keeping us down?

Is this why NIH gives more grant money to people over 70 than to people under 30?

Maybe we should all just quit and come back in 40 years, and see how science has progressed without us?

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Monday, March 17, 2008

Response to comments on last post

Stupid blogger is having problems posting my responses in the comment section. So here they are.

Anon 2:25,

Yes, several of us have suggested that mandatory retirement or some kind of senior advisory status (different from Investigator) might make a lot of sense.

They'd give up their lab space and equipment and exploiting their lab members, but they'd still be a great resource for oral history.

Most of the older scientists I know, that's all they want anyway. They want someone to tell them about their data, and ask their advice. Isn't that the most fun part anyway?

There are few faculty I know of who are genuinely doing the full job anymore at that age. They are all delegating to superdocs and grad students.

Anon 8:36,

I hadn't heard about Science Debate 2008, so I went and looked at the website.

I wish they'd debate stem cells, but they won't!

hee hee!

Agreed that most Nobel Laureates can't really speak to this issue.
I don't know any personally, although I've met a few, and I think it's fair to say their experiences are usually way out on the edge of the bell curve.

AAAS fellowship is something I've thought about pretty seriously, if this research thing doesn't work out. My fear is that it's the opposite of a postdoc- I don't think they just let you decide what you want to work on.

Anon 2:07,

I agree that it's totally idiotic to support people who got jobs during the least selective time over people who are coming in now (!). Totally stupid.

I know a few of these guys, and let's just put it this way: they're calling me and asking how to do experiments. I'm having to tell them they won't be able to publish without controls.

Yeah. Guys like that. Yippee.

I've always thought the definition of 'young investigator' was preposterous. Even sillier now as the age of 'young' is creeping up and up.

Anon 2:54,

Someone sent me a cartoon the other day, I wish I could post it but I can't reveal who it was. Basically they were saying their lab is having a hard time getting their RO1s renewed, because they already have >5 RO1s and several millions of dollars in funding, and not that many people actually working in the lab.


Oh and did I mention this is one of those labs where the postdocs write the RO1s, but they don't get credit as co-PIs?

Most, if not all, of the 'haves' I know of are exploiters in the extreme.

The worst of them are liars in the extreme as well, which is why they are the Haves.

But I've posted about that before.

The PIs I know who are on the older edge (I'm talking >60) are not training anyone enough to merit their enormous pay and mismanaged lab space;

none of them are innovative on their own, they just push through ideas that their lab members feed them;

and they're only productive in name because they get credit for the work of their slaves.


Let's put it this way. I was reading a book the other day and one of the characters visited a southern plantation sometime in the 1970s. She went on a tour of the place and there was no mention of slaves.

So she asked. "What about the slaves?"

And the tourguide said, with a straight face, that there weren't any.

So she took the tourguide over to the place where the slaves' graves were marked with single stones, and said something like , "Are you seriously trying to tell me you really think this tobacco plantation of >100 acres was farmed by a family of four?"

Needless to say, she ended up changing the way those tours were done, forever!

I realize our situation isn't quite as severe, but if you'll bear with the analogy, we need someone to do the equivalent "Are you seriously telling me you think these old geezers are actually writing all their own grants and coming up with all this innovation???"

Thursday, March 13, 2008

Remembering why science is fun.

I haven't been blogging much because I've been too busy having fun doing science.

Hooray! There's a phrase I can never use too much.

Had an adorable encounter with a visiting student who said my lab would be the one to join, and how soon would that be possible?

So cute. Wish I could have said 'soon'.

Otherwise, I'm enjoying, sort of, compiling mounds of data and making them into presentable formats.

I say sort of because it's still pretty tedious. I hate making sure everything is lined up perfectly and exactly the same size, but it has to be done.

I say enjoying because hey, I can put on my iTunes and whenever I finish something and print it out, it looks pretty good.

My main problem right now is actually also why I've always liked science: switching back and forth from visual to verbal and back again is really challenging.

It never occurred to me that this can be so hard, until recently when I was reading a book that described exercises for switching among the senses.

One of the exercises is perfect for most of us in a very zen way, regardless of your profession.

It was simply to practice throwing a ball up in the air, and catching it.

The idea is to think about how when you're throwing, that's active, and when you release it, that's passive. Waiting for it to come back down is observant, and catching it is making a connection.

Or something like that. I'm paraphrasing from memory here.

Anyway the point being that it's a lot like research. There's the wind up to the experiment, then putting everything in motion. Then you wait for the result. Then you have to figure out what it means.

I'm on the part where I'm building up to put the meaning out there, out in the world.

In a way it is putting a lot of things in motion.

It's very easy to just do experiments and never tell anyone about them. We all do it. The weird results that don't fit with anyone else's, the ones that we can't explain.

Some people are satisfied to stop at that point. (You don't want one of those people as your advisor!)

In the current climate, the process of putting it out there is at least as important, if not more important, than doing the experiment.

It has its own wind up (making the figures, writing the text, practicing the talk), delivery, waiting (especially if you apply for jobs!) and hopefully, if all goes well, making that connection.

I'm struggling with being in visual mode and then having to go into verbal mode. It's hard!

The wind up part can be really fun. Nobody is judging your data or your interpretation of it, and best of all, nobody is judging you personally.

But eventually they will. That part is scary.

In the meantime, you have to enjoy the part where you know something they don't know: you already know the answer.

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Saturday, March 08, 2008

On Devils and Details

My thesis advisor was fond of the phrase "the devil's in the details." I always took this to mean that the details, left undone, would come back to bite you in the ass.

I've since decided that this really is true in science, and it bites everyone (including my thesis advisor). But like most things in life, timing counts for a lot. If you can outrun the details, you can get away with leaving them out.

And knowing when a detail is a technical problem, or an exception to your model, is critical.

Sometimes chasing a detail is just a tangent. Sometimes it's the whole enchilada.


When I was learning how to write postdoc fellowships, my advisor told me that it was important to add enough detail to make it believable that you've really thought everything through. Of course the challenge, then, was not to take up too much space with minor points.

This was when I started to think a lot about emphasis. You want to highlight your main points, and then dress them up with just enough details. The trick was choosing the right details:

Not all details are equal.


More recently, I've noticed that my interdisciplinary interests are biting me in the ass, due to religious differences over the utility of details.

One discipline values details as a mark of integrity and thoroughness. Their papers tend to be solid, reproducible, and not in the Cell/Science/Nature journals.

The other discipline is quite the opposite. They value salesmanship. I'm pleased if I'm able to reproduce anything that has been published in that field, since it means it might not all be wrong.

To those people, salesmanship means glossing over, if not outright burying, details that don't fit with the prettiest version of their model.

They view people who pay attention to the details as mere technicians: people who must surely be missing the big picture.

Of course there is no correlation, so far as I can tell, between people who are good technically or who pay attention to details, and the ability to simultaneously think about the big picture. It's really a spectrum, like most human qualities. The two skills are not mutually exclusive.

I think the best scientists can do both the macro and the micro, the thinking and the hands-on part.

However, thinking about the big picture, and communicating the big picture, are two different things. That's where the sales skills come in.

Communicating the big picture is something some of us have to work hard to learn how to do. So I'm trying to figure out which details to hide on my slides, so I don't lose the people from the sales-heavy field - and just hope someone from the other field will ask if they don't believe me, so I can fill them in later.


I find myself trapped, since so far as I can tell, these sales people are largely Devils - when they're not outright lying, they're dangerously sloppy.

And I've had the unfortunate experience, perhaps because of my particular interdisciplinary bent, that leaving out any details tends to annoy reviewers and lower my credibility.

It matters which details you leave out.

Not to turn this into another rant about how corrupt our publication and funding and hiring systems are, but, let's face it. Most scientists can't handle the real truth: that many of their colleagues are desperate enough to be devils who bury the details that would ruin all their favorite models.

So I really have to wonder, if we held everyone to a higher standard, and really asked for all the details - could we get out of this state of denial where people are offended, rather than proud, to be asked?

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Alarming plagiarism of yours truly.

An alert reader pointed out that this person apparently ripped off, word-for-word (or nearly so), one of my posts.

It's worst than that, though, because there's more than one.

Unlike some of these websites that include the full text as well as some mention of MsPhD or YFS, this one doesn't credit me at all, so the posts appear as if they were original. Clearly, someone who didn't know about my blog wouldn't realize they're not reading the real thing.

I'm not sure what to do about this person, who goes by "The Mad Scientist".

I have to wonder if the other posts are also stolen from other people? It's really a shame, since some of them (besides mine, of course) are pretty good.

Are any of them original?

I always figured adding one of those copyright emblems to my blog would be silly, but maybe I will do that now.

In a way I'm flattered. But I would like to put a stop to it, and soon.

I think perhaps the most surprising thing to me is that the URL is also via

Shame on blogger for not having a way to catch this kind of thing automatically!

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Monday, March 03, 2008

Whether and when to quit grad school: response to comment on last post.

Dear Erin,

I feel so badly for you.

I am against people working in careers where they're miserable enough to need medication to function on a daily basis. To me that just says it's not a good fit.

That's not your fault, in my view, it's a problem with science in all of its un-touchy-feely current glory.

Ugh! Would that we could make it a little better, somehow! Blogging will have to do for today.

Of course I suspect some of the reasons you have anxiety, if not all, are the same things I blog about all the time.

We all just feel it to different degrees.

You must feel raw all the time, and that makes me sad.

I'm a little confused about how your advisor got you to work on a project that you found out later has nothing to do with your project. I guess it seemed related, but then you found out it can't go into your Master's thesis?

I'm also confused about whether your advisor has always been more on the supportive side and just recently became abusive (because what you're describing is, to put it mildly, taking advantage of you)?

Or was this advisor always like this (and therefore a major source of anxiety)?

Regardless, I think it's great that you have a job lined up. That gives you tremendous power.

I think you should try first to negotiate a way to get your degree before you give up. In this, though maybe not in all things (if they're like mine), your parents are right.

Here's the MsPhD part of the advice:

Perhaps you need to stand up to this advisor?

Perhaps that won't work in this case and you need to approach whatever passes for a graduate program/advisory committee where you are?

Figure out who has the power to give you what you want, and who is more likely to give it.

Being willing to walk away is very powerful.

In fact, it's the first thing they teach you in negotiating school (okay, so I've never been, but I've read some books).

I'd recommend getting a couple of good books on negotiating. As much as I badmouthed it recently, the one I just read might be helpful for you. It's called A Woman's Guide to Successful Negotiating: How to Convince, Collaborate, & Create Your Way to Agreement and you can get the e-version on Amazon instantly.

There are plenty of books like this out there, and it's worth your time to do this now, breathe deeply, and try to marshal your strength.

You do have some. It's in there.

And then, don't wait too long. Give it a shot. Ask for what you deserve. You want your degree? Say so. You don't have to be confrontational about it. You can work it in as part of another conversation.

Get someone to go with you if you need support, maybe a labmate or a mentor?

If nothing else, you will learn something from this experience.

Personally I hate to see someone go to grad school for 4 years and leave empty-handed, and I blame the advisors and the grad program.

I was actually just talking to a student today about accreditation, and she was saying that although they claim they want honest feedback, the committee that reviewed her program didn't seem like they would do anything about any of the problems.

So I also blame the accreditation process for letting it get this bad at this many places.

And with that, I have to go right now so I can't write more, but I'll keep thinking about you and see if I can come up with anything else.

I'm sure my gentle (!) readers will have more to say that might help you.

And I'm sure you're not alone, by the way. There are others just like you, probably reading this blog. Thanks for writing. I'm sure it will help them, too.

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