in the event, unlikely as it is, that you have not seen this, you need to.

A follow up Q&A with Baratunde

And Trump inserts himself and says he’s proud of the role he played, and says, “We have to verify this birth certificate. I have to take a look at this.” Historically, it’s quite dastardly, but not uncommon. For most of our history, any white person could grab any black person off the street and demand they dance. Or produce documents. Or kill that person, who wasn’t considered a person.
And Trump says he wants to just walk into the White House and touch this document? That he has the right to do so? You don’t have the right to do shit! You don’t have the right to roll up to the White House and say, “Show me your papers,” like it’s apartheid South Africa! In that, I could hear the voice of random white people in history, demanding money for my vote — wanting to know what’s my business in this part of town.

franscrollow Baratunde here.
h/t: Mike Dunford was on this early.

A: Labrador Retriever

April 28, 2011


Not as in “Fuck me!”. Nor even as in “Gee, what a fucked up situation”. More like as in

Fuck you, you fucking pitbull owners.

ALBUQUERQUE, N.M.—A New Mexico woman who witnessed four pit bulls fatally maul another woman on Easter Sunday said Thursday that she heard screams from inside her home, then rushed outside and saw that the victim had “big chunks missing” from her head and stomach and had arms that were bitten to the bone.

oooh, you say, musta been bad owners. poorly trained dogs. oh yeah?

Police Chief Patrick Gallagher has said the city hadn’t received any complaints about the dogs.

Q: Aren’t there some other dogs that you could own that would be just as nice of a pet?

In case you missed it, there is a great column up at Nature News by Professor Hidde Ploegh. It laments the ever increasing demands by reviewers of scientific manuscripts, particularly for GlamourMag level journals, for additional experiments.

Submit a biomedical-research paper to Nature or other high-profile journals, and a common recommendation often comes back from referees: perform additional experiments. Although such extra work can provide important support for the results being presented, all too frequently it represents instead an entirely new phase of the project, or does not extend the reach of what is reported.

The comments are shaping up quite nicely (also see my post at Scientopia) over there and I was struck by one particular contrast.
Maxine Clarke, Publishing Executive Editor (and listed fourth on the masthead) of Nature, issues a denial of culpability when she says:

Read the rest of this entry »

Things you learn.

April 27, 2011

The Internets are so awesomely entertaining that you cannot even wonder why there exists a PhD program in poultry science

A strong indicator of the fact that African Americans as a group continue to avoid most of the natural sciences appears in the statistics for specific disciplines. In 2004, 2,100 doctorates were awarded by universities in the United States in the fields of mathematical statistics, botany, optics physics, human and animal pathology, zoology, astrophysics, geometry, geophysics and seismology, general mathematics, nuclear physics, astronomy, marine sciences, nuclear engineering, polymer and plastics engineering, veterinary medicine, topology, hydrology and water resources, animal nutrition, wildlife/range management, number theory, fisheries science and management, atmospheric dynamics, engineering physics, paleontology, plant physiology, general atmospheric science, mathematical operations research, endocrinology, metallurgical engineering, meteorology, ocean engineering, poultry science, stratigraphy and sedimentation, wood science, polymer physics, acoustics, mineralogy and petrology, bacteriology, logic, ceramics science engineering, animal breeding and genetics, computing theory and practice, and mining and mineral engineering. Not one of these 2,100 doctoral degrees went to an African American.

or more specifically in chicken “products technology

The UGA Poultry Science Department offers specialized training in physiology, genetics, nutrition, products technology, parasitology, toxicology, microbiology and molecular biology leading to the M.S. or Ph.D. degrees in Poultry Science.

without starting some sort of a fight.

…or so says scientist Hidde Ploegh in a Nature News column.

The whole thing is brilliant and lays out the case admirably:

Rather than reviewing what is in front of them, referees often design and demand experiments for what would be better addressed in a follow-up paper. It is also commonplace for reviewers to suggest tests that, even if concluded successfully, do not materially affect conclusions….This has a serious and pernicious impact on the careers of young scientists, because it is not unusual for a year to pass before a paper is accepted into a high-profile journal. As a result, PhD degrees are delayed, postdocs may have to wait an entire year to compete for jobs and assistant professors can miss out on promotions…The extra months of experiments increase costs for labs, without any obvious advantage for science. Although journals profit handily when prospective authors offer the best science possible, most do not spend money to produce it.

The only glaring lack here is the failure to castigate this process for generating a LOT of data that may possibly be of use to science that will never see the light of day, once the extra person-years worth of work is shoehorned into a single additional figure.

The good Professor has three suggested solutions to help:

First, they should insist that reviewers provide a rough estimate of the anticipated extra cost (in real currency) and effort associated with experiments they request. This is not unlike what all researchers are typically asked to provide in grant applications.

This is a nonstarter to me. It just begs the question about how much additional effort and cost is too much and how much is just right. Who is doing to decide this part? Obviously the reviewers who are asking for the additional experiments have some idea already of the amount of time and expense…and they’ve made the demands anyway. Also, reviewers will shade their budget estimates in the direction of their demands “Oh, this should only take a month for a postdoc to work out”. Yeah right. I’m not seeing where this will help.

Second, journals should get academic editors with expertise in the subject to take a hard look at whether the requests of reviewers will affect the authors’ conclusions, and whether they can be implemented without undue delay.

This was my reaction to the column up to this point. The solution is good editing. I can’t tell you how many times at real journals (i.e., those who are focused on the science, not the chase to be first, hawt and/or sensational) that the editor has shut down reviewer requests for additional experiments to be added to our manuscripts. Sometimes explicitly by saying in the editorial part of the review “The request for additional experiments X, Y or Z by Reviewer #3 are beyond the scope” or sometimes implicitly “I concur that points A, B and C in the reviews are most important to address”. Either way, there is a clear signal that the Editor plans to accept the paper without the additional experiments. It should not surprise you that it is the practicing scientist class of Editor that I have found to engage in this behavior. They take an active role in policing the “level” of the journal not only in terms of keeping out the chaff but also in terms of keeping a lid on ever escalating demands for what is justified to publish as a paper.

There is another more cultural facet to the academic/professional editor discussion as well. I had a recent experience, as it happens, in which an editor eviscerated a manuscript we had submitted by demanding we delete a good half of the stuff in there. While it smarted to find that she did not recognize the unique brilliance of all of our offerings, I can accept this. This editor is a senior scientist in the field, has been an Editor in Chief of journals for a very long time and I am entirely uninsulted to find her inserting herself so emphatically in the process. I would have a considerably different reaction to the professional editor class which does not come with similar scientific stature (despite what they, hilariously, seem to think). So I’m with Professor Ploegh that this is a good change- academic editors (i.e., practicing scientist peers) over professional editors. You will be entirely unsurprised to learn that Nature editor Maxine Clarke is not impressed by this suggestion “I think your first and third suggestions, in particular, are good ones.“.

Back to Ploegh:

Third, reviewers should give a simple yes or no vote on the manuscript under scrutiny, barring fatal shortcomings in logic or execution. Once editors have decided that, in principle, the results are of interest to their publication and its readership (which is their editorial prerogative), passing a simple test of logical rigour and quality of data should be enough to get them through peer review.

He’s making a point consistent with his early observation that peer reviewers should stick to reviewing the manuscript that is in front of them, rather than reviewing the manuscript they think they’d like to see in the future. I concur. I think I’ve actually said this before in an exchange with some professional editor or other, probably Noah Gray of NPG, who tried to weasel out by insisting that editors are simply responding to the field (the peers doing the reviewing). As I noted above, academic editors have no problem telling reviewers who demand excessive numbers of additional experiments to go pound sand. There is no reason the professional editor class cannot do the same. Simply have a house rule that demands for additional experiments will be grounds for rejection of the manuscript. Not “revise and resubmit” trolling…rejection. “Try again later”. With the clear understanding that the present paper has been rejected and any subsequent submission better be substantially different. Because after all, that’s what the reviewer demands are saying, right? That it must be substantially different to be acceptable…

Professor Ploegh refers to a vicious cycle:

Many reviewers are also, of course, authors, who will receive such unreasonable demands in their turn, so why does the practice persist? Perhaps there is a sense of ‘what goes around comes around’, and scientists relish the chance to inflict their experiences on others.

So make use of this. Publish the papers that do not receive demands for additional experiments and give a hard rejection to those for which the reviews ask for lots of more stuff. Since GlamourScientists are the ones doing the reviewing, they’ll snap in to line eventually.

Professor Ploegh ends with a comment that is going to warm the cockles of the hearts of the younger scientists:

Having read some of the biographies of the founders of molecular biology, it is hard to escape the impression that, once, the mechanics of science were indeed thus. It is worth revisiting the experiment, I should think.

The nasty way to put this is that, dude, you OldTymers just walked around picking up fruit off the ground, never mind picking the low-hanging stuff, and it was a freaking Nature or Science paper. We’re up against some new astronomical standard in which a whole 5 year program of research is supposed to go into each GlamourPub.

The more sober realization is that science progressed just fine in the past when Science and Nature pubs with one or two figures in a “paper” of highly limited scope became foundational parts of our subfields. Certainly for those subfields of my own interest, when I go back to look at the original paper for something that became absolutely canonical it is a figure or two. A much more substantive paper always followed after the first observation but that was typically in a nonGlamour journal. A field journal. Now, of course, the followup papers are less frequently publishedby the original group*, and less frequently published at all**. That is a shame and a loss for science.

I can’t believe the NIH is not concerned that their money is being wasted with this competitive cycle being played out with their extramurally funded investigators, aided and abetted by GlamourMags with a clear profit motive.

*because, of course, being GlamourLabs, the filling in of “details” is best left for “the little people***” and they are on to the next big splash.

**why would some other group pursue an area that the GlamourLab has the lead on, they are just going to get scooped to the next paper (see vicious recursion with *)

**Yes, that is very nearly a direct quote of the Glamour-est PI of my acquaintance.

Standards and Practices

April 25, 2011

Language. For me, it boils down to language.
I’ll let the Big Dog fill you in:

Read the rest of this entry »

crossposting from Scienceblogs
Language. For me, it boils down to language.

I’ll let the Big Dog fill you in:
Read the rest of this entry »

A question arose on the Twitts recently where a newish investigator wanted to know if it was wiser to push earlier for his/her first senior author paper in a ~3-5 IF journal or hold out for a ~9 IF journal submission. It emerged during the ensuing Twitting that the person had about 10 months of some degree of independent funding under the bridge so far.

I had a post awhile ago (quite awhile) that I thought would cover my main point but it only touches on the idea of balancing your attack. The opening comment sets the right tone though.

My suggestion is, if you expect to have a career you had better have a good idea of what the standards are. So do the research. Do compare your CV with those of other scientists. What are the minimum criteria for getting a job / grant / promotion / tenure in your area? What are you going to do about it? What can you do about it? Don’t misunderstand me- nobody is going to hand you a job / grant / etc just because you hit the modal publication numbers. But it will be very easy for you to be pushed out of the running if you do NOT hit the expected values. So do what you can to keep your CV as competitive as possible.

And this, really, is the starting point to my answer to @chemstructbio. It is absolutely critical to understand within your own subfield, within the pool of investigators whom you consider to be your peers, what the standards are. Particularly when it comes to Impact Factor. In my fields of interest, the answer to this question is going to be quite simple. If you have zero senior author papers from your lab, and you have been at it with funding for coming up on a year or more, the priority for a 3-5 IF paper is absolutely acute*. If this is in reach and a ~9 IF is a stretch of more than a single review cycle, do the lower IF one. Now.

The reason being the idea of balance, and the difficulty your advocates have making a case for you when you give them nothing to work with. A society level journal publication is respectable for all but the snootiest of assclams. Respectable. An advocate can work with this. Published data can be argued on the merits. It is very hard to argue with nothing.

Yes, yes, yes. We all know what time it is on the street and how long it takes to get to that first ass-kicking paper. But when you are sitting there with the Biosketch…..evidence is the thing. Evidence of a published, peer-reviewed paper. Not in prep, not in submission. Accepted.

Now, if you have one already….then it is time to start balancing numbers against the IF against the real impact of the paper. Then you can afford it. But if you have none, my friends, it is time to get one.

*This is not saying that you are hosed if you do not have a senior author paper. Not at all. It’s just that it makes things go better. So if one is in reach, make it happen. It should be a huge priority, particularly if you have a little bit (or a lot) of funding in hand already. Because the reviewer demands for evidence of independent productivity will ramp up…clock’s aticking.

Happy 420 Dudes!

April 20, 2011

A little reading for marijuana fans from the blog’s Cannabis Archive
Yes, it does cause dependence, including symptoms of Withdrawal
A take on the conditional probability of cannabis dependence…wait, as many US folks are dependent on cannabis as have ever so much as tried…?
Oh, and that K2/Spice, synthetic marijuana stuff containing JWH-018 and other cannabimimetic full agonist drugs? Yeah that causes dependence too.

A peculiar phenomenon in some chronic marijuana users: Hyperemesis
The Pot Potency data
Parents want to know, “Did the pot make my kid lazy?


April 20, 2011

The notion that 30 minutes of sustained writing is “madwriting” as if it is some sort of miracle of concentration and productivity is fascinating.
If you had asked me before a day or two ago what I considered highly focused and concentrated writing, I would have said something around about 3-4 hour blocks. If I can get those in, I see some serious progress made on manuscripts or grant applications. Or animal use protocols, or biohazards protocols, or chemical hazards protocols.
And when I’m trying to hit a grant deadline, I’m going to need to put in several of these, anywhere from 5 to 10….and that’s when the writing is going well. Plus, I’ve been doing this for awhile so it isn’t exactly novel behavior…
Writing my dissertation? I was putting in 3-4 hour blocks of time one to two times per day for weeks. That was #madwriting*.
30 minute writing sprints?
Well, I suppose it is very good practice for 4pm on a grant deadline day when the admin says “Where’s the Abstract, Statement of Public Health Relevance and did you update the personal statement on your Biosketch?”
*there were circumstances. there usually are…
Additional Reading
The Twitter Phenomenon of #madwriting

From the NYT:

The University of North Dakota will face penalties for continuing to use its Fighting Sioux nickname and American Indian head logo, said Bernard Franklin, the executive vice president of the N.C.A.A. He said that a new North Dakota law requiring the university to use the nickname and logo did not change N.C.A.A. policy, which says the nickname and logo are offensive.

A new state law? Nice to know that this isn’t some historical accident but that they keep on refreshing their idiocy. Summary of North Dakota HB1263 (full text pdf)

The intercollegiate athletic teams sponsored by the university of North Dakota shall be known as the university of North Dakota fighting Sioux. Neither the university of North Dakota nor the state board of higher education may take any action to discontinue the use of the fighting Sioux nickname or the fighting Sioux logo in use on January 1, 2011. Any actions taken by the state board of higher education and the university of North Dakota before the effective date of this Act to discontinue the use of the fighting Sioux nickname and logo are preempted by this Act. If the national collegiate athletic association takes any action to penalize the university of North Dakota for using the fighting Sioux nickname or logo, the attorney general shall consider filing a federal antitrust claim against that association.

Well, well, well. Look at the vote count. Are you shocked that this was a mostly party-line vote?

Anyway the NCAA apparently left the University of North Dakota an out if…

it received approval from the state’s Spirit Lake and Standing Rock Sioux tribes.[from NYT article-bm]

In case you missed it, the “either” refers to me.
It might as well be the Washington Niggers

According to this, one of the named Sioux tribes voted to retain the name and the other tribe hasn’t weighed in yet. Interesting. Now I’m wondering why the state legislature didn’t just wait on the second tribe’s opinion?
Disclaimer: I may possibly be a lasting fan of a collegiate athletic opponent of one of UND’s NCAA-participating teams.

Comrade PhysioProf alerted me to a new entry in RePORTER:

DESCRIPTION (provided by applicant): Understanding the brain remains a great challenge for treatment of nervous system afflictions and humanistic reasons of comprehending the natural world. Basic neuroscience, though, is typically not taught until advanced college. We hypothesize such paucity in neuroscience education is due to the lack of simple, compelling, inexpensive tools for secondary school students to investigate and understand the brain. To address this need, we have invented the “SpikerBox”: a bio-amplifier that is easy-to-use, inexpensive (<$100), portable, and can detect and record the spiking activity (action potentials) of invertebrates such as crickets and cockroaches. We now aim: 1. To develop the full lesson materials including curricula, lesson plans, lab books, and assessments to allow our SpikerBox to be used in classrooms as an enabling tool to teach neuroscience. 2. To develop easy-to-use data analysis software to accompany the SpikerBox and allow basic neural analysis routines on an iPad or standard laptop. 3. To develop prototypes of the "RoboRoach," a kit modified from off-the-shelf remote control toys that mounts on a cockroach, delivers pulses to the antennae nerves, and allows remote control of cockroach locomotion. Such a preparation is a useful tool for teaching about microstimulation, electronics, and behavior. By allowing secondary school students to learn about the brain by performing real electrophysiology experiments in the classroom, we will increase understanding and retention of neuroscience concepts at an early age. As neuroscience is a multi-disciplinary field encompassing biology, mathematics, and engineering, our "SpikerBox" and "RoboRoach" kits may have the effect of improving performance in STEM-related disciplines and inspiring the next generation of scientists and engineers. PUBLIC HEALTH RELEVANCE: Backyard Brains will develop a "SpikerBox" kit with electronics, learning materials, and software to allow secondary school students to investigate the living nervous system of insects in the classroom. By allowing these students to do what was previously only available in advanced college, we aim to inspire the next generation of scientists, physicians, and engineers, as well as accelerate fundamental neuroscience research.

They’ve come a long way from a hilarious poster presentation on neuroscience in the wake of the coming zombie apocalypse, eh?
SBIR program of the NIH

Backyard Brains

Blogrolling: sex nerd

April 16, 2011

To be honest, I spent some time reading and I’m still trying to work out if this is scientifically informed, half-baked opinion blather, feminist sex lib stuff, or what.

Interesting threads though.

A recent Notice from the NIH (NOT-OD-11-064) indicates that there is a need to standardize and refine the appeal process.
Here’s what struck me on seeing this Notice pop up: I bet there has been a massive uptick in the rate of appeals since the sunsetting of the A2 and the threats to rigorously weed out thinly concealed revisions as “new” submissions.
One viewpoint on the wisdom of appealing the scoring of your grant proposal that is very common is captured in this comment over at the NIGMS blog:

Based on everything I have read about the appeals process on various Web pages of the NIH and Institute Web sites, it seems like you’d have to be extremely foolish and poorly informed to bother appealing.

NIGMS Director Berg responded:

Read the rest of this entry »

A comment over at FSP’s post on honorifics used for male and female acadmics triggers a thought. What is the proper address/honorific at, say, your kid’s school classroom?

FSP had said in the original post that she prefers “Professor” to “Doctor” in the academic milieu.

I think I would prefer “Doctor” to “Professor” in the non-academic setting, myself. It is funny isn’t it? “Professor” just seems like an honorific tied to the coincidence of my current job title whereas for some weird reason, “Doctor” seems to me like a more permanent and lasting attainment. Which, of course, it IS since in our current schemas it is highly unusual for anyone to stop being a “Doctor” through revocation of the degree. Otherwise, it is yours for life, once those five people let you back in the room and say “Congratulations Dr…”.

But why should Dr. seem so much more a permanent part of me that dictates what honorific people should use in normal daily life, in comparison with “Professor”? They are both just academic nonsense so why does it matter which one?