Archive for the 'Scientific Publication' category

Science magazine selects Jeremy Berg as EIC

May 25 2016 Published by under Science Publication, Scientific Publication

Well this is certainly exciting news!

Jeremy Berg, a biochemist and administrator at the University of Pittsburgh (Pitt) in Pennsylvania, will become the next editor-in-chief of Science magazine on 1 July. A former director of the National Institute of General Medical Sciences (NIGMS) who has a longstanding interest in science policy, Berg will succeed Marcia McNutt, who is stepping down to become president of the National Academy of Sciences.

I am a big fan of Jeremy Berg and his efforts to use data to drive policy when heading one of the NIH ICs and his efforts as a civilian to extract NIH grant data via FOIA requests for posting on his DataHound blog.

I look forward to a new era at Science magazine with an EIC who prefers that institutions make their decisions based on data and that they be as transparent as possible about their processes.

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More Neuroscience Smack

JNeuroJIF2014

I select these journals for comparison for a reason, of course. First, I'm in the addiction fields and Addiction Biology tops the JIF list of ISI Journal Citation Reports for the subcategory of Substance Abuse. Second, Biological Psychiatry and Neuropsychopharmacology publish a lot of behavioral pharmacology, another superset under which my work falls

The timeline is one of convenience, do note that I was in graduate school long before this.

When I entered graduate school, it was clear that publishing in the Journal of Neuroscience was considered something special. All the people presenting work from the platform at the Annual Meeting of the SfN were publishing relentlessly in JNeuro. People with posters drawing a crowd five people deep and spilling over the adjacent posters in an arc? Ditto.

I was in graduate school to study behavior, first, and something about the way the body accomplished these cool tasks second. This is still pretty much true, btw. For various reasons, I oriented toward the chemical communication and information transmission processes of the brain as my favored level of analysis. In short, I became a behavioral pharmacology person in orientation.

In behavioral pharmacology, the specificity of the analysis depends on three overarching factors. First, the components of the nervous system which respond to given drug molecules. Second, the specificity with which any given exogenous drug manipulation may act. Third, the regional constraints under which the drug manipulation is applied. By the time I entered graduate school, the scope of manipulations were relatively well developed. Sure, not all tools ended up having exactly the specificity that they were assumed to have. New receptor and transporter and intracellular chemical recognition sites were discovered frequently. Still are. But on the whole, we knew a lot about the interpretive space within which new experiments were being conducted.

I contrast this with lesion work. Because at the time I was in graduate school, there was another level of analysis that was also popular- the brain lesion. This related to a set of techniques in which regions of the brain were surgically deactivated/removed as the primary manipulation. The interpretive space tended to include fierce debate over the specificity with which the lesion had been produced. The physical area removed was rarely consistent in extent even within one study. Different approaches to the target might entail various collateral damages that were essentially ignored within a paper. The regions that were ablated contained, of course, a multitude of neuronal and glial subtypes and occasionally axonal tracts that were just passing through the neighborhood. Specificity was, in a word, poor.

I noticed very early in my days of grinding reading of my areas of interest that the Journal of Neuroscience just LOOOOOOOVED them a lesion study. And absolutely hated behavioral pharmacology.

I was, for a time, dismayed.

I couldn't believe it. The relative level of confidence in the claims versus the experimental evidence was ridiculously poor for lesions versus pharmacology. The designs were less comprehensive and less well controlled. The inconvenient bits of evidence provided early were entirely forgotten in a later rush to claim lesion/behavior impairment specificity. The rapid fire exchange of data in publications from the competing labs was exciting but really pointed out the flaws in the whole premise.

At the very least, you could trade one level of uncertainty of the behavioral pharmacology for an equally troublesome uncertainty in the lesion world.

It boggled my mind that one of these technique domains and levels of analysis was considered The Awesome for the flagship journal of the very prestigious and large Society for Neuroscience and the other was considered unworthy*.

Particularly when I would see the broad stretch of interpretive domains that enjoyed space and an audience at the Annual Meeting of the Society for Neuroscience. It did not escape my attention that the SfN was delighted to take dues and Annual Meeting fees from people conducting a whole host of neuroscience investigations (far, far beyond the subject of this post, btw. I have another whole rant on the topic of the behavioral specificity and lack thereof.) that would never be considered for publication in J Neuro on a categorical basis.

It has been a long time since my dawning realization of these issues and I have survived just fine, so far, doing the things that interest me in science. I may have published work once or twice in J Neuro but I generally do not, and can not. They are still no fans of what I think is most interesting in science.

It turns out that journals that are fans of behavioral pharmacology, see Figure above, do publish some of the stuff that I think is most interesting. They are accepting of levels of analysis that are most interesting to me, in addition to considerable overlap with the J Neuro-acceptable analyses of the present day. And as time has gone by, the JIF of these journals has risen while that of J Neuro has fallen. Debate the reasons for this as you like, we all know there are games to be played to change the JIF calculation. But ultimately, papers are cited or not and this has a role in driving the JIF.

I watch the JIF numbers for a whole host of journals that publish a lot more pedestrian work than these journals do as well. The vast majority are on slight upward trends. More science is being published and more citations are available for distribution, so this makes a lot of sense.

J Neuro tends to stand out as the only one on a long and steady downward trend.

If J Neuro doesn't halt this slide, it will end up down in the weeds of the 3-5 JIF range pretty soon. It will have a LOT more company down there. And it's pretensions to being the venue for the very best neuroscience work will be utterly over.

I confess I am a little bit sad about this. It is very hard to escape the imprinting of my undergraduate and graduate school education years. Not too sad, mind you, I definitely enjoy the schadenfreude of their demise.

But I am a little sad. This Journal is supposed to be awesome in my mind. It still publishes a lot of good stuff. And it deserves a lot of credit for breaking the Supplemental Materials cycle a few years ago. I still like the breadth and excitement of the SfN Annual Meeting which gives me a related warm fuzzy for the Journal.

But still. If they go down they have nothing but themselves to blame. And I'm okay being the natterer who gets to sneer that he told em so.

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*There is an argument to be made, one that is made by many, that the real problem at J Neuro is not the topic domains, per se, but rather a broader issue of the insider club that runs SfN and therefore the Journal**. I am not sure I really care about this too much because the result is the same.

**One might observe that publications which appear to be exceptions to the technique-domain rules usually come with insider-club authors.

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Complete stories, demonstrations of mechanism and other embarrassing fictions

There's a new post up at The Ideal Observer.

Many times you find people talking about how many papers a scientist has published, but does anyone seriously think that that is a useful number? One major factor is that individual researchers and communities have dramatically different ideas about what constitutes a publication unit.

Go read and comment.

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Review unto others

I think I've touched on this before but I'm still seeking clarity.

How do you review?

For a given journal, let's imagine this time, that you sometimes get manuscripts rejected from and sometimes get acceptances.

Do you review manuscripts for that journal as you would like to be reviewed?

Or as you have perceived yourself to have been reviewed?

Do you review according to your own evolved wisdom or with an eye to what you perceive the Editorial staff of the journal desire?

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Revise After Rejection

This mantra, provided by all good science supervisor types including my mentors, cannot be repeated too often.

There are some caveats, of course. Sometimes, for example, when the reviewer wants you to temper your justifiable interpretive claims or Discussion points that interest you.

It's the sort of thing you only need to do as a response to review when it has a chance of acceptance.

Outrageous claims that are going to be bait for any reviewer? Sure, back those down.

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Bias at work

A piece in Vox summarizes a study from Nextions showing that lawyers are more critical of a brief written by an African-American. 

I immediately thought of scientific manuscript review and the not-unusual request to have a revision "thoroughly edited by a native English speaker". My confirmation bias suggests that this is way more common when the first author has an apparently Asian surname.

It would be interesting to see a similar balanced test for scientific writing and review, wouldn't it?

My second thought was.... Ginther. Is this not another one of the thousand cuts contributing to African-American PIs' lower success rates and need to revise the proposal extra times? Seems as though it might be. 

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Strategic advice

Reminder for when you are submitting your manuscript to a dump journal.

Many of the people involved with what you consider to be a dump journal* for your work may not see it as quite so lowly a venue as you do.

This includes the AEs and reviewers, possibly the Editor in Chief as well. 

Don't patronize them. 
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*again, this is descriptive and not pejorative in my use. A semi respectable place where you can get a less than perfect manuscript published without too much hassle**.

**you hope.

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A new way to publish your dataset #OA waccaloons!

Elsevier has a new ....journal? I guess that is what it is.

Data in Brief

From the author guidelines:

Data in Brief provides a way for researchers to easily share and reuse each other's datasets by
publishing data articles that:

Thoroughly describe your data, facilitating reproducibility. Make your data, which is often buried in supplementary material, easier to find. Increase traffic towards associated research articles and data, leading to more citations. Open up doors for new collaborations.
Because you never know what data will be useful to someone else, Data in Brief welcomes submissions that describe data from all research areas.

At the moment they only list Section Editors in Proteomics, Materials Science, Molecular Phylogenetics and Evolution, Engineering and Genomics. So yes, there will apparently be peer review of these datasets:

Because Data in Brief articles are pure descriptions of data they are reviewed differently than a typical research article. The Data in Brief peer review process focuses on data transparency.

Reviewers review manuscripts based on the following criteria:
Do the description and data make sense? Do the authors adequately explain its utility to the community? Are the protocol/references for generating data adequate? Data format (is it standard? potentially re-usable?) Does the article follow the Data in Brief template? Is the data well documented?

Data in Brief that are converted supplementary files submitted alongside a research article via another Elsevier journal are editorially reviewed....

Wait. What's this part now?

Here's what the guidelines at a regular journal, also published by Elsevier, have to say about the purpose of Data in Brief:

Authors have the option of converting any or all parts of their supplementary or additional raw data into one or multiple Data in Brief articles, a new kind of article that houses and describes their data. Data in Brief articles ensure that your data, which is normally buried in supplementary material, is actively reviewed, curated, formatted, indexed, given a DOI and publicly available to all upon publication. Authors are encouraged to submit their Data in Brief article as an additional item directly alongside the revised version of their manuscript. If your research article is accepted, your Data in Brief article will automatically be transferred over to Data in Brief where it will be editorially reviewed and published in the new, open access journal, Data in Brief. Please note an open access fee is payable for publication in Data in Brief.

emphasis added.

So, for those of you that want to publish the data underlying your regular research article, instead of having it go unheeded in a Supplementary Materials pdf you now have the opportunity to pay an Open Access fee to get yourself a DOI for it.

20 responses so far

PLoS Has Angered the PastramiMachine!!!!

@pastramimachine is WICKED PISSED!

from the page charges (aka OA fee or whatever you want to call it. $2250 at PLoS Genetics according to this guy, I think it is still around $1350 for non GlamourHounds.)

So what has him so angree?

Dude, do you have the slightest idea what people make in the private sector? At the executive level? Of a company with $40-50 Million in gross revenue?

The median total compensation package for CEOs totaled $378,000.

The report says that companies with $25-49.9M in annual revenue are at the median for CEO pay.

I understand that academics don't get paid as well as they might be but....surely you have SOME idea of what private sector jobs pay? And say, what do University Presidents pull down, anyway?

So what? Is there any business that fails to advertise itself? In the hopes of growing in size or at least maintaining current revenues? Where's the evidence this is excessive? Have you any idea what PLoS is up against in terms of the advertising budgets of NPG, Springer, Elsevier, etc?

This is ridiculous. It's like asking your home builder why he doesn't have a lumbering operation and saw mill out in Oregon or up in Saskatchewan or wheretfever the 2X4s come from. This Aries Systems Corp is the outfit that built the EditorialManager system used by several academic publishers. It's a service provider. Why would the publisher of a journal re-invent the wheel?

Lobbying activities to keep Elsevier from playing penny-ante shenanigans with Congress to totally obliterate the requirement to deposit manuscripts in Pub Med Central, perhaps? Or related efforts? Sure, PLoS lobbying activities may be mostly for them but it seems that having a wealthy organization opposing the pay journals works out well for the OA fans. How can you complain about this, guy?

Maybe I missed something? When did PLoS say they weren't a company? And heck, many not-for-profit entities have investment portfolios. Starting with your local University (say, Rutgers, for example). What do you think the "endowment" is? This is no crime. This is responsible stewardship of a business entity. Building up a cushion against future changes in the business climate. Smart work, PLoS! Somehow I don't think PastramiMachine would be too happy if PLoS went belly-up and all of the published papers disappeared because there was nothing to pay the server fees with!

This guy is delusional, mostly because of his stated belief that PLoS is some sort of capital-gee GoodGuy. That's on you, dude, not on PLoS.

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More from Odyssey who picked out some replies from Michael Eisen.

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When reviewers can't relinquish their bone

Had an interesting category of thing happen on peer review of our work recently.

It was the species of reviewer objection where they know they can't lay a glove on you but they just can't stop themselves from asserting their disagreement. 

It was in several different contexts and the details differed. But the essence was the same. 

I'm just laughing.

I mean- why do we use language that identifies the weaknesses, limits or necessary caveats in our papers if it doesn't mean anything?

Saying "...and then there is this other possible interpretation" apparently enrages some reviewers that this possibility is not seen as a reason to prevent us from publishing the data. 

Pointing out that these papers over here support one view of accepted interpretations/practices/understanding can trigger outrage that you don't ignore those in favor of these other papers over there and their way of doing things. 

Identifying clearly and carefully why you made certain choices generates the most hilariously twisted "objective critiques" that really boil down to "Well I use these other models which are better for some reason I can't articulate."

Do you even scholarship, bro?

I mostly chuckle and move on, but these experiences do tie into Mike Eisen's current fevers about "publishing" manuscripts prior to peer review. So I do have sympathy for his position. It is annoying when such reviewer intransigence over non-universal interpretations is used to prevent publication of data. And it would sometimes be funny to have the "Your caveats aren't caveatty enough" discussion in public.

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