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October 26, 2012

If you’re still here I have up and joined Scientopia and will be posting there.

Update your whatnots.

Punting on Open Access

September 18, 2012

Not the concept, so much as the journals.

In my general field there seem to be two options in terms of Open Access journals. The Plos family of journals and another plos-like group. I submitted a paper to PLoS-ONE a while back. There were some issues. Despite the frequent claim of being more efficient than the ‘traditional’ journals my paper set a record for most amount of time “sitting on someone’s desk’. It took about 6 weeks, and some public complaining, to get assigned an editor. A process that traditional journals handle in maybe 5 mins.

Perhaps this is an issue with the breadth of PLoS. I’d previously considered submitting to the slightly more focused Open Access journal. That might have been a more suitable move.  Of course last week a lab mate told me that almost the same thing happened to him at that journal. The paper, sat and sat and sat, and then went out for review after ~2 months.

Not exactly accelerating academic publishing.

Both these of these journal groups make a big whoop about improving the publication process, in addition to being open access. That has not been my experience of that of many of  my colleagues. The experiences aren’t universally negative. There is some variety. But they certainly aren’t any better than submitting to traditional journals. I think I’ve come to the conclusion that I won’t be submitting anything to either of these journals. (I am writing this before my decision comes in for he PLOS paper, so it’s no influenced by that). Here’s my rationale:

1. They just don’t have the horses. PLOS-ONE seems to have three or four academic editors that may be interested in any research that I will be producing. Since at any point 2 or 3 may be on vacation, combined with the “only edit if you want to” opt in system. Seems like my papers are destined to “fall through the cracks”. This may be less the case at the more focused journal. I need to give their editor list a look through (maybe ask about their vacation schedule). If they have the same opt-in issue I will definitely be skipping them.

2. Traditional journals have their benefits. The high profile places I might submit all have triage systems that are very quick. I may seem odd to comment positively on a rejection mechanism, but I appreciate the efficiency. Time is valuable. The smaller more focused journals may take their time getting reviews, but I know what I’m getting. I “know” the people there and am confidence I can pick the right journal that will give my manuscripts a serious look.

3. Access seems to happen anyway. Much of my research is NIH funded and has to be put on in some form on PubMed. Also, in my area is seems pretty ubiquitous that papers are posted on lab websites. Submitting to traditional closed journals may not help the cause of Open Access, but as a practical matter my papers are pretty accessible to anyone vaguely motivated to get them.

Tea Leaves Reading

September 2, 2012

Way back in the early days of grant preparation I went on to NIH Reporter and printed out a list of the currently funded projects for the grant type. The profile of the projects being funded was not what I expected, yet not entirely surprising. I was reminded of course of the Bishop blog post on the devaluation of low-cost research. The profile of what NIH was funding (and what they weren’t) was certainly something I kept it mind in putting my project together for the grant. The degree to which my research program, and ideas for future projects resembled funded project should be accentuated.

That brings me to job ads. Some are quite specific in what they want. Others are vague. Others somehow manage a bit of both. It is tempting to try to do a bit of tea leaves reading here. Though many ads ask for a researcher of some broad topic, it is tempting read between the lines and assume they also mean using that hot new method everyone likes, or the one that we know NIH funds a lot. My own department wrote a pretty broad job ad last year, and then brought out 4 people with very very similar research methods (and proven or potential funding). I am waiting to see an ad that merely states Fundable researcher needed. Topic flexible. (I assume the ‘open’ searches are exactly this.)

Questions about science

August 9, 2012

I’ll have a real post one day, I swear. For now some pictures from Google auto fill.

Poll Experiment

June 18, 2012

Question: How long does it take to run an experiment? Just the data collection and basic analysis, assuming you could work exclusively on this one experiment. (if willing state your field in the comments).

For me it depends on what method I’m using, Method A is weeks to months, depending on the conditions. Method B is hours, but often includes weeks to months of pre-experiment work.

Using Excel graphs to fuel your existential crisis

May 21, 2012

Here’s how I’m procrastinating these days:

One of the local grads is having an existential crisis. I’m never going to get a job. I should never have come here. I shouldn’t have gone to grad school period. etc. etc. We’ll all been there. I attempted to cheer her up just as she hit the  “no job if your advisor isn’t famous” gripe. During that exchange she took advantage of my well known weakness for wasting spending time playing around with stats and got me to make a few graphs. Ok, so you don’t have to twist my arm for me to spend time on some analysis having nothing to do with my research. That’s how I ended up as a “statistical consultant” for a local coffee shop (they paid me in delicious sandwiches). Anywho, grad student got me to make the following:

(click to greatly embiggen)

Thats of representation of where the profs at some “top 5” department go their doctorates. Each line is one faculty, where the left point is the rank of the department and the right point the rank of that persons graduate alma matter (rank via usnews). The red dashed line is the median faculty. So the higher the slope the more a department takes faculty from higher ranked programs.

For comparison here are three other departments

Why have we made these graphs? I have no idea. They look pretty and we wanted to actually know where the profs at a few departments had gotten their doctorates (rather than rely on rumor and reputations).

the blog

May 11, 2012

Before I started posting here I’d been reading the science/academia internets for a few years. At some point while talking with another black science grad about her frustrations she asked me “so there are a few black science bloggers, right?” I drew a blank. Plenty people are pseudo-anon so who knows, but I couldn’t think of anyone visible. So I started1.

1. Since then I have found a few other science folks.

Secret Handshakes

May 7, 2012

I think I do a reasonable job of pursuing career development opportunities. Workshops, summer schools, etc. Not too long a go I became aware of two interesting opportunities. An APA solicitation for reviewers from “underrepresented groups” for any of their many journals, and the NIH Early Career Reviewer program.

I heard about both through “official” channels. The APA program was just a solicitation in a journal that I stumbled on. The NIH-ECR program information was forward to me by an NIH official. In both cases I (perhaps naively) assumed that the best way to purse each opportunity was to go though the process as written by the organization. Get your CV together and just apply as per the instructions.

Not sure that was a smart move.

The APA has yet to respond in well over a year. I resubmitted my application after 6 months of silence and even asked if the program was still ongoing. Nothing. Eventually I called them up to ask what the deal was. Long story short, the “program” amounts to them just forwarding your CV to a few editors. It is entirely possible (likley in my opinion) that my information was just ignored by the relevant editors, who I’m sure are overworked tenured folks. I can imagine that a “diversity reviewers” email might get a pretty low priority score behind their own pubs, grants, articles to review, grad students, etc etc. I asked if I’d get a better response by just contacting editors directly (“possibly”). Ok, then what’s the point of this whole thing? Not to make this post too long, but this is a wonderful illustration of the gap between meaning to nice things with regard to diversity and actually doing something.  This APA solicitation seems more “hey wouldn’t it be nice” than a serious attempt. I wonder if they keep track of how effective this solicitation is. Based on my experience I’d say, not very.

As for the NIH-ECR, I am still waiting a response (it hasn’t been that long), though I am not hopeful. I’m going to go ahead and contact an SRO directly. I have little faith that going though the application process will result in any sort of consideration or acknowledgement of my app. I think it’s interesting that others I’ve talked to on the science-internets think that talking directly to an SRO IS the standard procedure for this.

Both of these struck me as somewhat secret-handshake-ish. In both cases I took information from the organization about the opportunity at face value, only to later learn I was barking up the wrong tree. The real way to pursue these opportunities was something different, that I should have just known. Smart folks go through the side door, what you didn’t know about that, I thought everybody did. It’s exactly the kind of thing that can be bad for underrepresented folks. It’s kind of an odd possibility that both of these programs may be the least effective way of pursuing these opportunities.

Perhaps I just had a spell of naiveté. I am slightly annoyed at myself for not suspecting that there was a more direct approach available. Perhaps these sort of situations are unavoidable as organizations need flexibility  (e.g “letting SROs out into the wild). Still something about these two situations strikes me as slightly off.

Dr Bashir’s amazing impostor syndrome treatment

April 9, 2012

Not long a ago a friend of mine landed a TT interview at a Fancy Pants University (FPU). The interesting coincidence is was the same FPU I went to as an undergrad. So of course we chatted a bit before she went off for her interview. Unfortunately I couldn’t really provide her much useful information. I was a student in a totally different department. I had no idea what it’s like for professors1, let alone professors in her area. The conversation did have an interesting sequence that I’ll paraphrase:

“Sally”: What advice can you give me. How do you deal with the FPU arrogance?

Bashir: They’re arrogant?

Sally: Sure. Look who’s in that department that will be at my talk, Famous Researcher #1, Famous Researcher #2, etc.

Bashir: You’re worried about tough questions from them?

Sally: no…they’re hot shit. What if they think I’m an idiot?

Bashir: {bleep} them. You’re smart. Just act like you belong there.

Ok, perhaps my advice isn’t so much amazing. It was at least succinct and to the point. Cultivate a little bit of irrational confidence to inoculate yourself from impostor syndrome. Try it for a month, and call me in the morning.

1. Other than the one day my physics professor took time to explain his (failed) tenure case to class. Awkward.

Positive feedback for Scientists

April 4, 2012

Being a scientist is not a particularly positive experience. By design, most of the interactions are negative. Or I should say critical. That’s just how it works both on a grand scale and for each individual study. If scientists didn’t persist in providing negative critical feedback to each other, the grand enterprise would be much less efficient. That’s good for science. But for the individual scientist it’s kind of a downer.

I’m coming off a conference visit that included some good moments for me. People I’d never met had read my papers. Thought that the research I presented was interesting. Even cool. It was a very positive experience. So I thought, what can I do to facilitate that for other scientists? How can I help?

Here’s how. For the next conference I’m going to order up some Zazzle stickers with some positive feedback included. Hand them out at poster sessions or something.

I may need to pilot test them on my lab. See which ones work best.