Response to comments on last post

Kea -

I hoped this problem of "who really did what" would be solved by some journals' new policies offering some kind of statement of "author contributions", but it turns out that most of them don't allow for realistic categories.

For example, my advisor insisted on being listed as having helped in all areas, despite having actually FOUGHT ME EVERY STEP OF THE WAY and really only contributed to one aspect (editing the manuscript). But the reading audience won't know that. That includes the funding committees who award grants to my advisor based on my ideas and my persistence in making sure it got published.

Anon -

Personally, I think that kind of behavior would have to be really extreme before it would hurt you. Presumably you were being asked about this DURING INTERVIEWS? (in other words - CRY ME A RIVER?!)

We're all penalized by our advisor's bad publishing habits.

That was exactly my point.

SamanthaScientist -

This is the biggest trap with holding out for "kitchen sink" publications. MOST science has ambiguities that seem to occur in waves. The trick is publishing at the peak of the curve before you fall down into another confusion well, and the you climb back out and publish another paper with the next piece of the puzzle. There's a rhythm to it, if you know what you're doing and you can figure out how to break off story-sized pieces. That's how we make progress. The problem I see all the time is that you really need both sides: the person on the ground has one perspective on where the project is, and in the ideal situation, the person in the office (the PI) has a bird's-eye view of where the project begins and ends.

In practice, though, there are two major problems that I can see.

1. Conflict of interest

You want to publish and GTFO.

Your PI wants high-impact papers.

2. Poor Vision and Distrust

You don't have (much) experience with publishing, so you lack the vision and confidence to know how that's going to go. On the other hand, you probably read a lot, so you have some ideas about formats and journals based on what you've seen other people doing in your field. Still, you're supposed to trust your PI - even when your PI lets you down.

Your PI, on the other hand, probably can't stay on top of all the literature anymore, and probably doesn't even try. However, your PI also doesn't really feel comfortable trusting your opinion, either. After all, you are a junior trainee and WTF could you possibly know. Nothing, right?

This tends to lead to delays and, in the worst cases, stalemates that result in zero publications.

Meanwhile, you're waiting or trying to prove your point so you do more experiments. Or your PI doesn't trust you so you're told to do more experiments, presumably with the hope of clarifying some things (but as we all know, more experiments does not always mean immediate clarity!).

This just ends up muddying the waters.

Personally, what I've learned to do is go a little farther than I think I need to, and test the waters. If it's muddier down there, I pull my toe out and publish, knowing I will come back and wade through the mud later when I have my hip-boots on.

If it's getting clearer and I can see lots of pretty fishies, I keep going and catch as many fish as I think I can fit in the paper. (assuming I have the resources I need, etc. which I don't anyway but that's a different rant!)

There are all kinds of tricks to writing good manuscripts, too, and I can't say I've learned how to do this. But the most successful scientists seem to know how to lead their reviewers in the direction of the pretty fishies so that the reviewers will say, "Hey! Fishies!" which is exactly what you want them to do.

Those of us who are less adept at leading the reviewer (and our advisors) tend to try to point at the fishies and end up with reviewers and advisors who love pointing at the muddy snake-pit and saying:

"Why don't you take off all your clothes and flail around in there for a while?"

advisor horror stories re: publishing

As per the latest post over at FSP, here are some relevant posts re: publishing troubles with unreasonable advisers.

Publishing Overview

Slightly less amusing version of publishing overview

Before submitting:

Who did the work?

Writing nonsense

Fun with formatting

Babysitting

Extreme cases

Bias

Credit where credit is due

Emphasis

After you get the reviews:

Rebuttal Letter

Minor Adjustments

Your work is not your own

that fits - now I'll have to look her up

took this silly quiz by way of GrrlScientist.

I am: James Tiptree, Jr. (Alice B. Sheldon) In the 1970s she was perhaps the most memorable, and one of the most popular, short story writers. Her real life was as fantastic as her fiction.

Which science fiction writer are you?

a good news/bad news scenario for my readers

the book is coming along.

I started looking into Amazon digital publishing. It's either that or the sort of thing that FSP used. But I like the idea of having a Kindle book.

Have to figure out the legalities of using people's real names in a tell-all memoir. (read: I think I will need a lawyer)

don't know how much more blogging I'll be doing.

please continue sending your questions and comments and I will try to respond. I'll probably still see things on other blogs that inspire me to write here. For a while anyway.

the blog is not going anywhere. but I need to move on. when I can't even read that Dr. Brazen Hussy has job interviews without being jealous of her, or read the kind and encouraging comments from readers who say they hope I will get the job I want, it is time to stop torturing myself.

it's funny because one of the commenters asked why I don't have impostor syndrome about my ability to run a lab, like that was a bad thing. I thought that was weird and backwards.

but the truth is I am tired of living as a closeted blogger. Writing is one of the most rewarding things I do, I need it like air, but nobody knows I do it and nobody here knows this is me.

I kind of have impostor syndrome about being a writer, but it's backwards. It's closet fever.

so in the hopes of getting out of the writing closet, I am working on the book and plotting exit strategies.

thanks for your thoughtful input and continued participation over the years. it has been fun, and enlightening, and I'm pretty sure I wouldn't have made it this far in science without blogging and the support of the blogging community.

unfortunately, it looks like none of the sacrificing has paid off, and tenacity can't fix a certain amount of cumulative career damage.

so here I'll write what I often feel: maybe the most useful thing I've ever done for science was writing this blog.

good luck to you all

- MsPhD

More on presentations (also some ranting about writing)

By way of FSP's latest post, I wanted to say something more here since she had 44 comments already and many were quite long.

Lately there's been a lot of talk about "why do young women drop out" of the academic pipeline.

Lately I have been hearing from a lot of young women about why.

(As an aside: I've covered all but one of these topics (I think extensively?) on this blog from my own point of view. This post is mostly about the other one I really haven't covered.)

The why includes many components, but I think the main ones are:

1. not feeling welcome
2. wanting kids
3. wanting job security
4. outright harassment
5. wanting more money

Let's pick #1-2 for the sake of addressing FSP's post.

There is still a lot of pressure, especially in the US, for women to have children and be supported primarily by their husband.

I've had many long discussions with friends from Europe about the nonsense of last names, taxes, and mortgages in this country. On the one hand, we supposedly have equal property rights as men. Nobody would say, nowadays, that a woman could not legally own her own house. However, some of the red tape might lead you to think otherwise, especially if you are married.

I think one of the things we underestimate in science is how many young women feel these pressures. Constantly. From their own families, and from their in-laws.

They already feel left out of science as it is, socially speaking. Many fields are still majority male at the upper levels, even though we have this constant stream of young women coming in... and then leaving again. They see their friends leaving. It's a sinking ship. And they are not stupid.

There's still a lot of talk among young women about things like:

1. should I tell my boss I'm pregnant?
2. when's the best time to be pregnant in grad school/postdoc/junior professor (before my ovaries dry out)?
3. should I expect to be treated badly because I'm going on maternity leave (yes)?

They get the answers and they start making other plans for their lives.

So in response to FSP's question, no, I don't think it is too much information (aka TMI) for a (presumably senior, tenured?) professor to include in her research seminar some (?) mention about how she integrated having a family with having a career.

I think one of the major problems, as bluntly illustrated by the comments on FSP's post, is that women are often just as sexist and discriminatory as men are.

And many of the senior women in science now came from a generation of all-or-nothing. They did not have children, and whatever their feelings about it now, they tend to resent younger women just for having the choice. And they're not very sympathetic when their own students or postdocs need time off before or after having a child, or when they need more flexible schedules. I've seen it; I've heard about it; and you know it's true. Having a female PI is not necessarily any better.

I'll admit, learning to recognize the resentment and where it comes from can be really difficult. In my case, I have a younger friend who is very very girly. When I first met her I was mostly surprised that she wanted to hang out with me. Then sometimes I was slightly bothered by her girly-ness. But I was able to take a step back and say, you know what? She's being herself. In that very Legally Blonde kinda way that I actually really respect and enjoy. And I'll admit I'm a little bit jealous that she has figured out a way to do it without being the slightest bit self-conscious.

I would love to see more of this in science.

I think there has been a dangerous trend lately, perhaps brought on by various linguist-type philosophers (Roland Barthes comes to mind), to pretend as if science is written objectively by using pronoun-free passive phrasing. (Bear with me here, it's a short tangent and I promise it's relevant.)

Science was never like this. Looking back, historically science grew out of letters people wrote to each other (yes, there were women doing this too) about things they did basically as hobbies. Gardening, collecting bugs or rocks, looking at stars. They were conversations. They wrote, "I saw this. I thought that. I think it means blah. Next I think I'll do bleh."

Science now might as well be done mostly by robots, since so much of it is repetitious anyway. So then it might make sense to use phrasing like "The DNA was sequenced and this analysis revealed" rather than, "When we examined the DNA sequence, it became apparent that."

End of tangent. My point is that a little person-ality is not bad for science. It's actually how science was always done until very recently (say the last 20 years or so). So I'm very concerned when I see this kind of backlash against scientists being people. The two should not be mutually exclusive.

Sure, by the time you're a tenured professor you might have had all the life beaten out of you. You might have squeezed yourself into the mold so hard you cut off all the parts that didn't fit. But is that really what you want for the next generation?

Personally, I would MUCH rather have an informal presentation from a friend about her work, where she intersperses in stories about what else was going on at the time. Because that's where ideas come from, really. And science is sorely lacking for ideas these days- precisely because we're driving away so much young talent in the form of young women who haven't lost or traded in all their personality.

There's hope for you yet

Just finished reading a somewhat fatalistic post over at FSP about teaching science writing (and whether it can be taught).

One particular comment caught my eye, and I wanted to write a long response so I will copy that comment here (with apologies to the author, but hopefully my response will make it worthwhile):

Anonymous said...

Oh it would be so super helpful to get some tips on how to get a grip on all this writing.
If people have any suggestions on good books to teach yourself writing..... it would be grand to share those.

I am just in the process of writing / correcting my thesis and it is all done, but according to my supervisor, the quality of the writing (not the analysis) is not so good. And I need to seriously work on this because I will fail if I cannot manage to make myself understandable to other people.... (I know she has a point, but sometimes it is hard to improve, especially since the rest of our department is a bit more laissez-faire and never gives critical feedback) :(

I think for me it is not the grammar and the writing as such. But the following points:

1) What are the exact words/expressions one should use - I seem to memorize the broad concepts and the full story rather than single definitions and their respective relations. My brain just seems more wired like that, so it is sometimes hard to translate from one "language" to the other.

2) One of the main points of my supervisor is that I try to cramp to much information into one sentence or half sentence. I should rather keep it clear and short instead of crowded and too challenging.
The reason for this is (I think): I very often feel that what I did was fully trivial and not really that interesting. So that basically everybody would just be able to glance over it and think: "oh, yeah, sure, easy, so what is your point?". By cramping stuff in, I try to prove, that I actually do know my stuff.

3) And sometimes I am just helpless in separating the relevant bits from the not so relevant bits. Discussing the stuff with other people would help and actually does help, but only if I am not under major stress (because they are important people, because there is only little time, because I am having a major self-confidence crisis) :(

4) also, because I feel I should be able to do it just like that, I probably also spend far too little time on structuring and writing well formulated sentences than I should.... (well my fault really).

I'm going to start by saying, this comment is written very clearly. You got your points across very well. So I think you have all the right tools. Also, this comment really resonated with me because you sound a bit like me when I was a grad student.

1. What are the exact words/expressions one should use - I seem to memorize the broad concepts and the full story [...] so it is sometimes hard to translate from one "language" to the other.

I had this same problem, and sometimes have it even now (and probably always will).

The truth is, if you're working on something relatively established, then yes there is specific language, and it is used a certain way by convention. You can learn this by reading papers in your field. Many of the comments on FSPs site were spot-on with this kind of advice. I particularly liked the suggestion to pick a few good papers in your field and dissect them.

But if you are working on something new, or if you are on the edge of something old and venturing into something new, you might find examples of things that are poorly defined. In those cases, multiple people use the same words, but they are sloppy about it. That is confusing for you as a reader, and very confusing if you want to write about these things but you are not exactly sure what to call them.

I ran into this during my thesis work. I was working on something that had a name. It was very well established, so it was in the textbooks with this name and diagrams, etc. But as it turned out, nobody agreed on what that name meant at the molecular level.

It turns out that the secret to science writing is also the secret to science reading: most people are taught to avoid, at all costs, ever mentioning where their work raises more questions than it answers.

So if something is not known, we are taught to NEVER say at the end of the results section of a paper:"this is still not known and will require further investigation". That is the kiss of death if you want your work published!

We are also taught to NEVER say in the results section of a paper "this is controversial."

So if you really want to know what has been done and what hasn't, you have to learn to pay attention to what is NOT said. You have to figure out what was NOT DONE. What was NOT SHOWN?

It's part of human cognition that we fill in gaps using intuition. The trick is to get enough distance to know the difference between assumptions and testable hypotheses.

Also, another thing you might try that works well for me, is going back in time.

Go back to what you thought before you started your project - because it changed as you went along. "Before" is where you audience is. They don't know what you know.

I find it helpful to go back and ask myself that eternal question in a very serious way: what was I thinking when I started this project?

For my thesis, I had to take a step back, review the old data that came before my project, and decide:

a) what was really known before
b) what was really not spelled out about the missing bits
c) what do I know now that can help me fill in the missing bits
d) how do I say that clearly.

Note that the hard part comes BEFORE the "saying it clearly." I always say the hardest part of writing is the deciding.

This brings me to the next point you bring up.

2. By cramping stuff in, I try to prove, that I actually do know my stuff.

We intuitive types tend to make what others call "logical leaps" (I can tell from what you wrote that you are like me in this regard).

We have to learn how to slow down and spell things out, precisely because they are so obvious to us.

The secret here is: these "obvious" things are not obvious to most people. And you are probably making connections that others have not really made. It's hard to see this when you're inside your own head, so the only way I've found to get out of this trap is to take several steps back.

Students tend to assume that when you write as a professional, grownup scientist, you are writing for the other experts in your field. But this is almost never the case! The best scientists are always writing for experts in OTHER fields. Think about it this way: there are not enough people in your field for them all to serve on a study section dedicated only to your little subject area. No. Most of your grants will be reviewed by people who work on something else!

With that in mind, think of the audience for all of your scientific writing as other smart people who took the basic four AP/college-level science courses (intro bio, intro chem, intro physics, and calculus). That's about the common ground we have across fields.

So you don't have to spell out absolutely all the basics, but almost. I think at the beginning it is helpful to practice spelling out every single thing, if nothing else than to name the assumptions YOU are making, about what is obvious, and what is really known.

Yes, at the beginning you will feel like you are writing for 5th graders. Like you are writing a dictionary. You will feel as if you are being condescending. You will get over this feeling, but it might last a while. At the beginning, you are just aiming to be clear and not get ahead of yourself. It will be boring, and you will want to jump ahead. But you have to make yourself do it without skipping any steps. You know if you randomly skip steps in a protocol that your experiments don't work, right? It's the same thing with writing.

Eventually, as you become more practiced, you'll be more comfortable with thinking of it this way: you're writing for new grad students.

You want them to see why you like your topic, and why what you did is cool. It has to be accessible enough for them to understand it without looking up every reference you cite.

And it is good to over-write, at least in the first "vomit" draft. Write EVERYTHING at the beginning. That is what editing is for. Which brings me to your next point (which I am separating into 2 parts for clarity!).

3a. And sometimes I am just helpless in separating the relevant bits from the not so relevant bits. Discussing the stuff with other people would help and actually does help

Yes. This is where giving lab meetings is good. But if you don't get to do this very often, or don't want to do it yet, there are other ways to get where you want to go.

Talking to strangers about your project is great practice. And when I say strangers, I mean people on the subway. People you meet in the waiting room outside the dentist's office. Random people. Also, talking to friends from home who are not scientists is really useful.

You will find that even people who initially sound excited when you say you are a scientist get bored really fast, so you have to get to your point quickly and sound exciting (!), and/or you have to make a simple analogy with something in daily life. Even the most obscure things can be explained by a cute analogy.

Even if you can't use your cute analogy in a Very Formal Written Document, it is a useful exercise for focusing your thinking.

For example, for my work I have the "please ask me more" accessible answer, and the "please don't ask me more" inaccessible answer. I use them depending on my mood.

So if I want to be friendly and show what a generous martyr I am:

Me: "I work on X disease (which affects your grandmother and killed your cat last year)"
Them: "Really! What exactly do you do?"

If I want people to leave me alone:

Me: "I work on bloggedy-ology thing you've never heard of" and I make no effort to explain what that is.
Them: "Oh" (and then walk away).

So you see what I mean? The same thing happens with writing. You want people to understand enough that they feel engaged and want to know the answers to the obvious questions (which you fed them)!

So this "talking to strangers" exercise will help you answer the following questions:

1. What is the coolest thing I did in science
2. Why should anybody care
3. What is the one thing I want them to remember when I am done talking about this

Even better is to explain it to someone, say a non-scientist or a younger student (undergrads are great for this!) and then listen to them explain it to a third person.

Yes, it will be awkward and probably comical at first. But it will help you understand how to teach your subject, which is essentially what you're doing when you write about it.

You are teaching what you did, why it is cool, why they should care, and what is the take-home message.

You just happen to be doing it on paper in a relatively stylized and potentially soon-to-be-outdated format. ;-)

3b. but only if I am not under major stress (because they are important people, because there is only little time, because I am having a major self-confidence crisis)

Okay, this is a separate issue. Who are these so-called "important people"? Don't talk to them yet.

Like I said, find other people. Talk to your family, your dog, your neighbor. Talk to a tree. Seriously. I always practice my talks alone before I give them, and I always talk about my work before I write it up. This means my laptop monitor has heard a lot of my random babbling (and it still loves me! Awww).

It also means I get a lot of my awkwardness out before I talk to real people, especially before I talk to important people.

You think articulate people are always articulate? No way, no how. The best speakers and writers I know all practice, practice, practice what they will say, and they edit how they will say it.

Then, when you get some of that precious quality time with Important People, you won't be shy because you'll be well-rehearsed and comfortable talking about your work in a succinct little soundbite (theoretically, anyway).

4. also, because I feel I should be able to do it just like that, I probably also spend far too little time on structuring and writing well formulated sentences than I should.... (well my fault really).

This is not really how it's done. The best, most efficient writers I know all do a "vomit" draft, written conversationally just like you wrote this comment. Just the way you would talk to a friend.

Then you go back and see if the logic makes any sense. See if you skipped over things and didn't spell them out.

Then you go back and spell everything out.

Then you go back and see if all the missing bits are really filled in, or if you missed a few more. And then you fill those in.

At the VERY END, you go back and work on re-structuring your sentences.

But plan on several rounds of drafts and editing, editing and drafts.

Structuring your sentences will not help with the overall organization if you're getting ahead of yourself and not spelling things out. Gotta see the forest for the trees. Then you come back later and fill in the veins on the leaves.

Oh, and one final point, now that I've droned on and on and on.

There are many kinds of writers, but it is VERY hard to find good editors. If your advisor is saying "not so good", that is not constructive feedback. That is vague, negative criticism without specific suggestions for how to improve!

Personally, I am on the warpath against these PIs who think that re-writing every sentence is "teaching". ARGH!

There are some good books about how to be your own best editor, so I recommend starting there. Also, consider asking some other not-too-important but friendly people to give you feedback about where you're making sense and where you are going off on tangents.

There endeth the lecture. Go forth and scribble!

Just for the fun of it?

Been thinking a lot again about the old "art for art's sake" part of doing science. In other words, just to know the answer, even if no one else knows or cares.

This is very similar to the pressure of blogging vs. writing just because I enjoy writing. Almost every time I sit down to write lately, I debate whether I should be writing here at all, or if I shouldn't just be writing in my journal for writing for my self's sake.

This analogy got me thinking again about the Journal of Visualized Experiments (as in, "By JoVE, I think she's got it!"). It hasn't really caught on yet, at least not in my little corner of science. But ever since it appeared, I've had real hope that it will fill a serious hole in science.

The thing is, no matter how carefully done, there is really no substitute for doing the experiment yourself, or short of that, witnessing it (live or recorded). JoVE is the opposite of science for science's sake: it's science for everyone else's sake.

My frustration with my PI lately mostly stems from this central problem of trust. My PI does not watch me do experiments. Therefore, my PI, being a control-freak, does not trust my results. Does not trust my skills as a scientist. Does not trust me.

And yes, after all the hard work I have been doing, yes that is depressing.

But it's not just my PI. I spend a lot of time trying to figure out how to convince not just my PI, but my scientific "peers" and "colleagues" (aka competitors and reviewers) that my results are real. They may be stranger than fiction, but the data are what the data are. And I might not be able to explain it all right now, but the default setting assumes that I can't be trusted to have at least, in good faith, done the best I could with the best of what's available right now.

And nevermind the part where I should be given a chance to continue to try to figure it the rest of it out, because I'm really the best person to do that.

But given all the hurdles to getting your science seen and respected by everyone else, wouldn't it be easier to just do it until you yourself are convinced? And screw the part where you're working your ass off trying to convince everyone else, when they're not even open-minded enough to appreciate how hard you've been working?

Especially if there's no jobs anyway? What the hell difference does it make if I piss away what's left of my funding just amusing myself playing with scientific toys until my time is up?

I wonder how many people are daily asking themselves these kinds of questions? Is it just me?

Lately I'm not sure what gets me to lab everyday. Sheer work ethic, I guess, to bring home a paycheck and health benefits, if not any sense of accomplishment or respect.

Sometimes I try to console myself that, even if it doesn't work well enough to convince anyone else, I should try to have fun doing it, at least maybe that would restore some sense of personal accomplishment (even if it's not professionally recognized). Sometimes this works, at least temporarily.

But I think the central hypocrazy is that constantly having to worry about how to convince everyone else is sucking all the fun out of it for me.

Is this what it's like for the rest of your career? Always worrying about what everyone else thinks? Or is it really true that you can hide in your little corner, do your little thing until you think it's good, and then put it out as an offering when think you can't possibly make it any better?

This is the part of mentoring that I never got. My thesis advisor was a hide-in-corner type. The GlamourMag wannabes tend to be the crowd-pleasing type. Guess which type has more funding?

I can't figure out how to reconcile these. The cycle is wearing me out. Here is a stripped-down version of how things have gone for me. This was sort of an interesting exercise. Maybe some of you will recognize it as familiar:

1. Have exciting idea for a way to answer a cool question.
2. Do experiment. Have fun doing it!
3. Get exciting result. Feel slightly nervous that it might never work again.
4. Mock up figure. Try to contain excitement.
5. Repeat experiment somewhat nervously.
6. Get reproducible result! Hooray!
7. Revise figure, rejoice in the scientific method!
8. Present figure to various people (including PI).
9. Receive criticism from various people (including PI). Feel slightly deflated but still determined.
10. Perform different experiments to address criticism, slightly annoyed but mostly confident that they will be consistent with original result.
11. Mock up supplemental figures.
12. Repeat supplemental experiments.
13. Get reproducible supplemental data. Phew!
14. Revise supplemental figures. Rejoice that the scientific method works!
15. Draft manuscript. This part is fun, too.
16. Submit manuscript to PI. Don't expect an immediate response, but need a break from looking at it myself.
17. Time passes. No response from PI. Not a big surprise.
18. Present work to other people; ask for comments on manuscript draft.
19. Receive feedback from other people (no response from PI). Some of the feedback is very positive! This is fun too!
20. Approach PI and ask if/when draft will be read.
21. Perform additional experiments as per feedback from other people. That was helpful; rejoice in the scientific community!
22. Get additional results. Make additional figures and supplemental figures.
23. Revise manuscript. Yes, glad we did that, but no, these additional results did not change the point of the paper. Maybe it is a stronger claim.
24. Resubmit revised manuscript to Journal of PI's Desk.
25. Commence Nagging.
26. PI reads manuscript, does not understand it.
27. Long meeting with PI. Leave thinking PI understands somewhat better.
28. Repeat steps 18-27.
29. Commence reading books on Negotiation.
30. Attempt to convince PI that it's time to submit manuscript.
31. Repeat steps 18-26.
32. Consider quitting science.
33. Write blog; visit therapist; cry a lot. Think about alternative careers.
34. Diagnosis major depression. Make appointment with psychiatrist.
35. Repeat steps 18-32.
36. Watch peers from other labs gets papers accepted into High Impact Journals.
37. Repeat steps 32-33.
38. Get asked if I'll be applying for jobs this year and did that paper ever get published?
39. Repeat steps 32-33.
40. Avoid confronting PI for fear of bursting into tears, yelling, or both.
41. Repeat steps 36-40.

Unfocused

Can't seem to put together an idea for a post. Have lots of wispy thoughts that get away... can't seem to smush them together to make one big one worth writing about.

Lots of unbloggable little tidbits lately. Lots of personal stuff that I have realized, having made the mistake before, that I don't really want input on from the blogosphere.

Speaking of input, I will write a little about that, since I am a little curious about what other bloggers think about this issue.

Been reading a book by a writer who talks about how she never reads reviews of her work, doesn't want to know that people write book reports on her novels, doesn't want to know what they think because she just writes for herself.

Got me thinking about the good and bad of having comments contantly coming in on one's writing, as happens on blogs.

I guess this writer would not like to have a blog.

But it does make me think again about the good and bad of having constant input on the main writing outlet that I use regularly (aside from my private diary, which rarely contains any great revelations, though sometimes amusing gossip).

Writing is, in many ways, a form of breathing for me. Sometimes worrying about being anonymous and/or criticized for what I write here makes me feel, well, really stifled and self-censoring. And I get more than enough of that in lab, thank you very much.

Which isn't to say that I never have anything to write about that I want other people to read. I do, pretty frequently, want to write for the express purpose of communicating with the vast faceless audience of desperate, often clueless students considering science as a career. To say what I wish I had known when I was their age; what no one else will say; what most don't really believe could possibly be happening, but it does happen. To be a vocal witness to the atrocities. To document what happens to me, and what I see happening all around me.

It didn't start out that way. I really wanted to write about how cool it is to be a scientist. But somewhere along the way that got lost in all the awful things that have happened to me while I was trying to do science. What is that saying? Life is what happens while you're making other plans?

Anyway since I'm of two minds about the good and bad of blogging, for others vs. for myself, I guess I'll try to stop writing myself around in circles on this topic. There is definitely something existentially strange about writing a post and then getting almost instant feedback.

Usually, I love what I wrote and it feels great to write it and re-read it.

But sometimes, no one else likes it and I get a deluge of angry comments. Sometimes that bothers me for days.

Other times I don't care what you say, any of you, and I just delete the annoying ones and go on with my day. Sometimes I laugh a little as I do that and wish that I could do the same thing when people in real life criticize me, especially when they do it anonymously. Wouldn't it be nice to have a delete key for paper and grant reviews?

Other times I just sort of toss something off and then get lots of praise for saying how many of us feel, apparently, although I was really just writing what I was thinking and not really worrying how it would read (at least, not too much- I've been blogging long enough that I always think about who is reading this).

And then sometimes I'm just really glad that somebody appreciated it, because it feels like a freebie, a nice little bonus for doing something I wanted to do anyway. Sort of how I wish scientific publishing would be, but it never has been that way for me.

And maybe the thing that worries me is whether blogging regularly is actually stopping me from doing other kinds of more creative (read: also potentially more therapeutic) writing, because there's only so much time in a day and even being very unfocused, I can only do so many things at once.

Poll of the day.

Random email asking you to contribute to a document (sort of being a survey participant). You won't be an author, but you'll be acknowledged. Do you
	a) Insist on authorship and offer to write a chunk of it (need the line on the CV!)
	b) Take the offer as is and just do it
	c) Decline politely and see what happens
	d) Decline not so politely and see what happens
	e) Google the person and try to find someone who knows them
	f) e and, if it's for real, then a
	g) e and, if it's for real, then b
pollcode.com free polls

Blog frequency and topics.

In a book I'm reading, there was this random off-topic observation about a new theory on journaling.

The thinking now goes that writing only about bad things is bad for your mental health.

Apparently it is now believed that it is healthier to write regularly (every day) no matter what.

I guess this could be because it forces you to take note on days when nothing particularly interesting or otherwise bad has happened (?).

It really had not crossed my mind how much writing can act to reinforce our ideas, both consciously and unconsciously. In the process of writing these blogs, I do read and re-read what I've written, and edit, and re-write, and repeat. In the process, my words do get into my eyes and ears.

So I'm curious about this theory, and I might try to find out more about it. In some ways I guess it makes sense.

I certainly had not considered that only blogging when the mood strikes might be bad for me somehow.

Sometimes the mood is funny or at least darkly humorous, but there are lots of days when things are basically fine and I just have nothing interesting to say. And this year especially I have not been blogging every day.

So I don't know if it would help me much to write something every day, even if it's not particularly pithy or insightful. But it would be worth it to do the experiment, since it might have a dual purpose: to help allay the erroneous perception seen often in the comments, that I am my blog in real life.

I'm not trying to be my blog persona. But maybe blogging is adversely affecting me psychologically in ways I never considered.

And here I thought blogging was an outlet. Maybe it's just a form of electronic wallowing that actually makes me feel worse without my knowing it.

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.




Newsflash:
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.

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.

REALLY??

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?

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.

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?

Paper pieces.

Somebody really needs to write a science-specific program for compiling papers. Soon, please?

Here's what I'm doing right now, and I'm not joking about this:

Step 1: Drafting using Scrivener . Scrivener is great, I love it. But it can't do references or formatting.

Step 2: Export from Scrivener into a word processor, e.g. Pages or the trial version I downloaded of Nisus Writer. But neither of these can do references.

Step 3: Attempt to create new library of references in Endnote. I used to be able to get it to connect to Pubmed and download the papers into it that way, but for some reason today the searching function wasn't working and the program kept crashing. After 5 tries, I gave up because I didn't really want to use Word anyway.

Step 4: Rapidly and easily create new library of references in BibDesk. Yay! I love BibDesk. I love the new search function, it's super-fast and way better than Endnote. The only drag for me was I had one paper from pre-1968 and the search function couldn't find it. It's online but apparently not in Pubmed. So I had to put it in by hand. Yippee.

Step 5: Convert paper to LaTeX by hand using old templates from last (still unpublished) paper and (still unfunded) grant application. The good news is, the program will automatically put in all my references, format everything, etc. when I TeX the paper. The bad news is, the intermediate version looks like a computer program, and my co-authors will panic if I give them that.

But overall this is pretty ridiculous. While Scrivener can import other file types, there's no linkback to let you open and edit your figures easily in their native applications, e.g. Photoshop or whatever else you use.

And I don't really like the solution that you can export your text as an .rtf file from Scrivener or Nisus and then run it through Endnote after the fact- that's just lame and you have to do it over and over if you change anything?? Not gonna happen.

I love the corkboard feature in Scrivener, I use it a lot. But they should give you the option to write in corkboard mode instead of having it be separate from the text.

Scientific writing is basically always the same. Even the paragraph format could have a template. Why don't we just use templates? It's so ridiculous that we spend all this time on formatting, especially if you're going to submit a paper and then rapidly resubmit to other journals if it doesn't go out for review! Somebody needs to make an easier WYSIWYG program that can let you make custom templates and share them. What do you think? That would be a lot easier and a huge timesaver, right???

And differences that really waste your time are things like whether figures are labeled Figure 1. or Fig.1 and whether the components of figures are labeled with capital A , B, C or lowercase a, b, c and whether they're bold or not or (in parentheses) or not.

Personally, I don't care much about typesetting unless it's inconsistent. But I know some reviewers (and editors) get ticked off about stuff like that.