Archive for the 'Academics' category

Supplementary Materials practices rob authors of citation credit

This is all the fault of qaz. And long time reader Nat had a blog post on this ages ago.

First, I shouldn't have to remind you all that much about a simple fact of nature in the academic crediting system. Citations matter. Our quality and status as academic scientists will be judged, in small or in large ways, by the citations that our own publications garner.

This is not to say the interpretation of citations is all the same because it most assuredly is not. Citation counting leads to all sorts of distilled measures across your career arc- Highly Cited and the h-index are two examples. Citation counting can be used to judge the quality of your individual paper as well- from the total number of cites, to the sustained citing across the years to the impressive-ness of the journals in which your paper has been cited.

Various stakeholders may disagree over which measure of citation of your work is most critical.

On one thing everyone agrees.

Citations matter.

One problem (out of many) with the "Supplementary Materials", that are now very close to required at some journals and heavily encouraged at others, is that they are ignored by the ISI's Web of Science indexing and, so far as I can tell, Google Scholar.

So, by engaging in this perverted system by which journals are themselves competing with each other, you* are robbing your colleagues of their proper due.

Nat observed that you might actually do this intentionally, if you are a jerk.

So now, not only can supplementary info be used as a dumping ground for your inconclusive or crappy data, but you can also stick references to your competitors in there and shaft them their citations.

Try not to be a jerk. Resist this Supplementary Materials nonsense. Science will be the better for it.

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*yes, this includes me. I just checked some Supplementary citations that we've published to see if either ISI or Google Scholar indexes them- they do not.

25 responses so far

Careful with your manuscript edits, folks

via Twitter and retractionwatch, some hilarity that ended up in the published version of a paper*.

Although association preferences documented in our study theoretically could be a consequence of either mating or shoaling preferences in the different female groups investigated (should we cite the crappy Gabor paper here?), shoaling preferences are unlikely drivers of the documented patterns both because of evidence from previous research and inconsistencies with a priori predictions.

Careful what sorts of editorial manuscript comments you let slip through, people.

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*apparently the authors are trying to correct the record so it may not last in the official version at the journal.

9 responses so far

A sports-analogy for ASBMB President McKnight

Nov 04 2014 Published by under Academics, Diversity in Science

Steven McKnight is simply intoxicated with his first taste of a social media imbroglio.

...inclusion of the volatile word [riff-raff] in the C3 essay prompted widespread attention. For this, I am simply delighted. This was my first brush with social media, and I can clearly see its power.
...
My next two essays, for the December and January editions of ASBMB Today, will deal with this flaw head-on. Trust me — I will take off the gloves and fight bare-fisted in those two essays.

I'm sympathetic. We all get a little giddy the first time we spark a social media dustup that gets all sorts of people talking about us and our pet opinions. Doesn't make him any more right in his opinions, but whatever.

What really interests me is his choice of a sports-analogy that is more apt than he realizes.

In the state of Texas, tens of thousands of young kids begin competing in organized football during elementary school. The enterprise is highly inclusive and exceedingly diverse. By the time these kids get to high school, they know a lot about the sport and have begun to develop skills. In high school, however, a weeding-out process begins. Not all kids make the junior varsity and varsity teams, and not all kids — even if they make the team — are apportioned equal playing time. As things progress to college, the weeding-out process becomes all the more acute. Playing on Friday nights as a high-school athlete in Texas is lots of fun with broad participation. Playing on Saturdays as a college athlete may be equally fun, but only the most competitive kids are on the field. The final weeding-out step comes when players are drafted by the National Football League — 32 teams sport 53-man rosters, meaning that only 1,696 young men are eligible to suit up for Sunday football. These are the best of the best athletes and are rewarded accordingly....I think of science in this same way.

Emphasis added.

Naturally this is just a re-hash of the baseball player analogy that Comradde PhysioProffe loves to deploy on these pages and it has a lot of truth in it.

I wrote a post once upon a time that is relevant to this issue. HIGHLY relevant.



WarrenMoonEdEskimosHmm. You know, I once watched a Rose Bowl in which an undersized mediocre looking, but nevertheless competent, quarterback did a decent job of not losing too badly to his opposition. Faint praise right? Well, homie went on to a NFL pro career and made tons of cash while being, well, still kinda mediocre. Back in the 1978 Rose Bowl, however, fans were lucky enough to watch one Warren Moon (Wikipedia) of the UW Huskies whup up on the U. Mich Wolverines (boo!). Of course, even for some third rate collegiate bowl game, the fans were lucky to have him.

He was recruited by a number of colleges, but some wanted to convert Moon to another position as was the norm for many major colleges recruiting black high school quarterbacks.[9] Moon decided to attend West Los Angeles College in 1974-75 where he was a record-setting quarterback. After Moon showed his ability at West L.A., only a handful of four-year colleges showed interest in signing him. Offensive Coordinator Dick Scesniak [University of Washington], however, was eager to sign the rifle-armed Moon.

...oh, for chrissakes! People. This was the 1970s!!! Oh yeah, that's right. I remember those days. Black players can't be quarterback, you see. Don't have the right shoulder structure, it's a genetic thing doncha know. Plus, they aren't as good at all that, you know, quarterbacking stuff....
Come to think of it, I seem to recall some weebag Div I hockey player (who never ended up going anywhere professionally) writing some paper about how black people's hip structure precluded them from skating very well. (Or, skating like gangbusters and then fixing, oh, knees and hips for a living as an orthopedic surgeon)

Sorry. Back to the point. Oh yes. Warren Moon. Back to the Wikipedia:

Throughout his CFL career, Moon amassed 1,369 completions on 2,382 attempts (57.4 completion percentage) for 21,228 yards and 144 touchdown passes. He also led his team to victory in 9 of 10 postseason games. He was inducted into the Canadian Football Hall of Fame in 2001 and the Edmonton Eskimos Wall of Honour. In 2006, he was ranked fifth on a list of the greatest 50 CFL players presented by Canadian sports network TSN.

Not to shabby for a guy thought physically and mentally incapable of playing the quarterback position because of his skin color, right? Pretty decent.

What? What's that you say? There's more? Oh, riiiiigghht. That Warren Moon. The one who next jumped to the NFL and played from 1984-2000 as one of the more exciting quarterbacks to take the field,

Combining his NFL and CFL stats, Moon's numbers are nearly unmatched in professional football annals: 5,357 completions in 9,205 attempts for 70,553 yards and 435 touchdowns. Even if his Canadian League statistics are discounted, Warren Moon's career is still exceptional: 3,988 completions for 49,325 yards, 291 touchdown passes, 1,736 yards rushing, and 22 rushing touchdowns. During his NFL career, Warren Moon was named to nine Pro Bowl games (1988-1995, 1997).

I'm just getting going...

Alright. There's really not much point in going on and on to list Owens and Ashe and Gibson and the Williamses and Ribbses and Woods and Jones and all the other great athletes who thrilled (or continue to thrill) us with their class, competence and courage. Little point in detailing for each case where and when the operating rules of their sports (official and/or de facto) would have (or did..or still do) prevent them from excelling because of their skin color. Not much profit in describing how the overt bigotry of "they can't do it" papered over the fear that someone might be better than the rest of us. Silly to talk about the moral repugnance of categorically closing off the open field of play to some people just to benefit ourselves or those more like ourselves.

Because, you know, we're beyond all that sort of thing now. And...this is a blog that is supposed to focus on science. And the conduct of science. Which is objective. The only goal is the discovery.


To spell it out for Dr. McKnight and his fellow travelers....

Science is not a pure meritocracy. In the recent past when current generations were getting their start academic science was even less of a pure meritocracy. People who didn't look the right way, choose parents in the right way, express external dangly bits in the right way....all sorts of people who might have come to the table with the right brain equipment were systematically excluded. Denied from the competition before it even properly got started.

This still goes on. The "weeding-out" process that McKnight refers to (sports and science alike) is affected by bias. Opportunity is afforded to not the purest demonstrable talent. The pool of talent is chosen by the coaches. If they don't think a black kid can play quarterback, they will do their damndest to convert him to some other position so as to keep his "talent". How many Warren Moons did we never get to see on the field taking snaps?

As the man said, I think of science in this same way.

The coaches are the lab heads. The grayer bearded and bluer of hair. The gatekeepers are supported by their peers in review, in conference program committee and on hiring committees. Just as assuredly as coaches are supported by their owners, boosters, loyal alum, etc who have definite opinions on what a quarterback should be.

Somewhat less categorically, the coaches of sports and the coaches of science have individual biases as well. Show early signs of talent or even just effort.... and the coach gives you more playing time, calls the plays to you and lets you take the crunch-time shots. Sometimes the favored player is clearly inferior but the coach likes them for some reason (often enough because it is their own child) and wants to give them the best shot. Sometimes specialist talents are not used effectively simply because the coach can't see it or doesn't know how to work this talent into the mix so as to benefit the team (and that specialist talent's development).

I see this all the damn time in my now considerable hours spent watching my kids and their teammates play various sports.

And you know what? It is JUST like a dynamic that goes down in larger academic labs.

It is JUST like a dynamic that goes on in scientific sub-fields.

And McKnight's vision of who the "riff-raff" are and who the real scientists are cannot help but be similarly biased. We can't speculate on the nature of McKnight's biases...who knows, he may think that women or African-American or Asian scientists are the bomb and that standard old American white-guys like himself are a played out demographic*. I don't know**.

But what I do know is that whatever his concept of who is in the "riff raff" pool, he is biased and wrong. How can he not be? Most any individual person is going to be biased. That is why we use grant-selection and faculty-selection processes that depend on a committee of people. So as to hedge our bets against the bias of the individual attitude.

So I welcome this discussion McKnight would like to have. I look forward to further "bare-fisted" assertions of his position.

Because you know what? I know guys like this. I know what they are.

And I'm here to tell you. This guy is going to reveal further depths of his indefensible, personal-bias based and just-plain-wrong attitudes about who the best scientists are. In doing so, he will undercut support for anyone who might be nodding along with his truthiness at present. And that will be a good thing.

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*I do actually know at least one highly accomplished privileged older white guy scientist who has expressed a sentiment like this and appears to believe it. Just for the record.

**HAHAHAHAHA, of course, I do know. This guy is going to get caught saying some horrible racist and/or sexist thing along the lines of Jim Watson's finest statements. There is no possible other way this can go down. It's a rule of nature.

44 responses so far

Klingon University

Nov 03 2014 Published by under Academics

The best known Klingon proverb

Revenge is a dish best served cold.

is proof that before they were warriors, the Klingons were academicians.

4 responses so far

Datahound on productivity

This final figure from Datahound's post on K99/R00 recipients who have managed to win R01 funding is fascinating to me. This is a plot of individual investigators, matching their number of published papers against a weighted sum of publication. The weighting is for the number of authors on each paper as follows: "One way to correct for the influence of an increased number of authors on the number of publications is to weight each publication by 1/(number of authors) (as was suggested by a comment on Twitter). In this scenario, a paper with two authors would be worth 1/2 while a paper with 10 authors would be worth 1/10."

Doing this adjustment to the unadjusted authors/papers relationship tightens up the relationship from a correlation coefficient of 0.47 to 0.83.

Ultimately this post shows pretty emphatically that when you operate in a subfield or niche or laboratory that tends to publish papers with a lot of authors, you get more author credits. This even survives the diluting effect of dividing each paper by the number of authors on it. There are undoubtedly many implications.

I think the relationship tends to argue that increasing the author number is not a reflection of the so-called courtesy or guest authorships that seem to bother a lot of a people in science. If you get more papers produced, even when you divide by the number of authors on each paper, then this tends to suggest that authors are contributing additional science. The scatter plots even seem to show a fairly linear relationship so we can't argue that it tails off after some arbitrary cutoff of author numbers.

Another implication is for the purely personal. If we can generate more plots like this one across subfields or across PI characteristics (there may be something odd about the K99/R00 population of investigators for example), there may be a productivity line against which to compare ourselves. Do we (or the candidate) have more or fewer publications than would be predicted from the average number of authors? Does this suggest that you can identify slackers from larger labs (that happen to have a lot of pubs) and hard chargers from smaller labs (that have fewer total pubs, but excel against the expected value)?

15 responses so far

Boomer academics plan to never, ever retire

Sep 26 2014 Published by under Academics, Anger

Somehow I missed this in the Inside Higher Ed a year ago.

Some 74 percent of professors aged 49-67 plan to delay retirement past age 65 or never retire at all, according to a new Fidelity Investments study of higher education faculty. While 69 percent of those surveyed cited financial concerns, an even higher percentage of professors said love of their careers factored into their decision.
...
For the faculty boomers who will delay retirement due to professional reasons, 89 percent want to stay busy and productive, 64 percent say they love their work too much to give it up, and 41 percent are unwilling to relinquish continued access to – and affiliation with – their institution.

USBirthsIn related news, this chart tells you about the size of the Boomer, X and Millennial generations in the US. Hint, look at the total-births trace. This has very real consequences. We see the effects of the Boomers in many job sectors, of course, but the academic science one is a job sector which encourages the hardening of generational privilege. People do not become too physically worn out to work. They clearly want nothing other than to die as an active member of the workforce. They simply persist.

At present, the oldsters/Boomers are a huge part of the distribution of the Professor class.

They have a disproportional and distorting effect on everything.

When they DO finally die off then the replacement will come from the Millennial generation. So big ups there, o complaining millennials! The future is bright.

Sourced from the CDC.

h/t: Neurorumblr

82 responses so far

Faculty Recruitment by Trolling K99 Awards

Sep 22 2014 Published by under Academics, Careerism

Remember back in high school (for USians) how you received a deluge of college recruitment literature just after your PSAT and SAT scores hit the streets? Maybe I'm misremembering but it seemed as though colleges (and the Armed Forces) had access to the databases somehow and could target their recruiting.

I have heard rumour of search committees sending out letters to recent K99 awardees and inviting them to apply for open faculty positions.

Anyone else hearing anything like this?

29 responses so far

People of science are just like other people. Horrible.

Sep 19 2014 Published by under Academics, Anger, AntiFeminist Asshole

Go read comments from Professor Isis-the-scientist today:

Science Has A Thomas Jefferson Problem...

Still, this doesn’t change the fact that the notion that “Science Has a Sexual Assault Problem” makes me salty. Life has a sexual assault problem. 26% of women scientists are assaulted in the field, but about that many women in general report sexual assault. A large portion of the attacks against scientists are perpetrated by someone the victim knew, but many women in general know their attackers. So, at the crux of the stunning and shocking and eye opening is something that I find more insidious – it is the belief that science is somehow different than society at large.

After all, surely rape and assault and violence are acts committed by poor people, and brown folks, NFL players and the occasional misguided frat boy. Certainly our logical, skeptical, professional and enlightened scientific brethren aren’t capable of the type of violence that Hope describes. Surely, tenured white women aren’t at risk for that type of violence.

Pretending that any type of person is "different", in the good way, is a suboptimal way to go through life.

People are horrible.

Given half a chance:

-Doods will try to rape women
-White cops will shoot innocent teen browns
-Dewds will try to cop a feel.
-Grant and manuscript and career/job reviewers will support candidates that seem most like themselves
-Guys will leer and objectify.
-Postdocs will slack and blame their PI
-Old wrinkly profs will delusionally think one of the young sweet grad student things will come back to their shitty hotel room at scientific meetings if their clumsy overtures are made to enough of them.
-PIs will exploit the hell out of their "trainees"
-Men will rape women.
-Institutions, meaning deanlets, will screw over their Golden Goose Faculty

People are horrible.

Act accordingly.

20 responses so far

NPRonNIH continues: The Postdoc

More from Richard Harris at NPR:

Too Few University Jobs For America's Young Scientists

That's because if you want a career in academia, it's almost essential as a postdoc to make a splashy discovery and get the findings published in a top scientific journal. Hubbard-Lucey is working on an experiment that she hopes will be her ticket to a professorship — or at least to an interview for an academic job.

Whether she succeeds or not, she's part of a shadow workforce made up of highly qualified scientists who work long hours for comparatively little pay, considering their level of education: about $40,000 a year.

Potnia Theron wishes to discuss this last assertion: NPR story on Postdocs: what is your salary? edition.

And, I am glad she found a position in NYC. I am sure she loves The City. But $47K is a lot more than median salary in the United Sates right now. Maybe its not enough to live in NYC, but it is elsewhere.

I have an older post for your consideration of what trainee salaries look like compared to when I was a wee trainee. My conclusion that scientific trainees enjoy a 30% or more bonus in inflation-constant dollars over my day was not of any comfort to the Millennial types, apparently. So good luck with your point, Potnia.

Anyway, you'll be happy to know the subject of the NPR piece came out okay in the end:

That first conversation took place in May. Later in the summer, while Hubbard-Lucey was still working on her scientific paper, she heard about a job where she could make good use of her Ph.D. She wouldn't be running a lab or working in academia. But she would be advancing cancer research at a nonprofit institute. She got the job. And now, she says, she's happy with the new path she's chosen.

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Way to blow the lede, Richard Harris. Way to blow the lede.

176 responses so far

"I'm sure we can put it on the Training Grant..."

Aug 28 2014 Published by under Academics, Postgraduate Training

LOL

18 responses so far

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