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.