Archive for the 'Scientific Publication' category

Nature publishes overwhelmingly proven "NEW AMAZING FINDING" ....because optogenetics!

The PR headlines are breathless and consistent:

Researchers Identify Brain Circuit That Regulates Thirst

Brain’s On-Off Thirst Switch Identified

The paper is here.

Yuki Oka, Mingyu Ye & Charles S. Zuker Thirst driving and suppressing signals encoded by distinct neural populations in the brain Nature (2015) doi:10.1038/nature14108

The takeaway punch message from the Abstract:

These results reveal an innate brain circuit that can turn an animal’s water-drinking behaviour on and off, and probably functions as a centre for thirst control in the
mammalian brain.

Somebody like me immediately thinks to himself "subfornical neurons control drinking behavior? This is like the fifth lecture in Psych 105: Introduction to Physiological Psychology."

Let's do a little PubMed troll for "subfornical drinking". Yeah, we've known since at least the 1970s that the subfornical control of drinking behavior is essential, robust and mediated by angiotensin II signalling. We know how this area responds to blood volemia and natremia and how the positioning relative to the third ventricle and the function of the circumventricular organ vis a vis the blood-brain barrier permits this rapid-response. We know the signalling works through AT1 receptor subtype to excite subfornical neuronal activity via electrophysiological recording techniques and genetic deletions. Cholinergic mechanisms have likewise been identified as critical components via pharmacological experiments. Mapping of activated neurons has been used to identify related circuitry. The targets of subfornical neurons are known and their involvement in drinking behavior has likewise been characterized. Extensively. We know that electrical stimulation of these neuronal populations activates drinking in water sated rats, for goodness sake! We know there are at least three subpopulations of SFO neurons involved and something about the neurochemical signalling complexity.

There are review articles that you can read if you want to get up to speed.

The new work by Oka and colleagues simply repeats the above-mentioned electro-stimulation experiment from 1983 using optogenetic stimulation. Apart from this, maybe, we have an advance* in that they identified ETV-1 vs VGAT (GABA transporter) markers of two distinct subpopulations of neurons which have opposite effects on the motivation to consume water.

That's it.

This paper is best described as a very small, incremental advance in understanding of thirst and drinking behavior, albeit tarted up with the pizzaz of optogenetic techniques.

Yet it was published in Nature.

Someone really needs to introduce the editorial staff of Nature to PubMed.
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*BTW, a Nature editor confirms this microscopic incremental advance is what is new about this paper.

49 responses so far

Thought of the Day

On the resetting of the date of original submission:

One thing it does is keep a lid on people submitting a priority place holder before the study is even half done. I could see this as a positive step. Anything to undermine scooping culture in science is good by me.

One response so far

Are your journals permitting only one "major revision" round?

Skeptic noted the following on a prior post:

First time submitted to JN. Submitted revision with additional experiments. The editor sent the paper to a new reviewer and he/she asks additional experiments. In the editor's word, "he has to reject the paper because this was the revision."

This echoes something I have only recently heard about from a peer. Namely that a journal editor said that a manuscript was being rejected due to* it being policy not to permit multiple rounds of revision after a "major revisions" decision.

The implications are curious. I have not yet ever been told by a journal editor that this is their policy when I have been asked to review a manuscript.

I will, now and again, give a second recommendation for Major Revisions if I feel like the authors are not really taking my points to heart after the first round. I may even switch from Minor Revisions to Major Revisions in such a case.

Obviously, since I didn't select the "Reject" option in these cases, I didn't make my review thinking that my recommendation was in fact a "Reject" instead of the "Major Revisions".

I am bothered by this. It seems that journals are probably adopting these policies because they can, i.e., they get far more submissions than they can print. So one way to go about triaging the avalanche is to assume that manuscripts that require more than one round of fighting over revisions can be readily discarded. But this ignores the intent of the peer reviewer to large extent.

Well, now that I know this about two journals for which I review, I will adjust my behavior accordingly. I will understand that a recommendation of "Major Revisions" on the revised version of the manuscript will be interpreted by the Editor as "Reject" and I will supply the recommendation that I intend.

Is anyone else hearing these policies from journals in their fields?
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*having been around the block a time or two I hypothesize that, whether stated or not, those priority ratings that peer reviewers are asked to supply have something to do with these decisions as well. The authors generally only see the comments and may have no idea that that "favorable" reviewer who didn't find much of fault with the manuscript gave them a big old "booooooring" on the priority rating.

47 responses so far

Is the J Neuro policy banning Supplemental Materials backfiring?

As you will recall, I was very happy when the Journal of Neuroscience decided to ban the inclusion of any Supplemental Materials in articles considered for publication. That move took place back in 2010.

Dr. Becca, however, made the following observation on a recent post:

I'm done submitting to J Neuro. The combination of endless experiment requests due to unlimited space and no supp info,

I find that to be a fascinating comment. It suggests that perhaps the J Neuro policy has been ineffectual, or even has backfired.

To be honest, I can't recall that I have noticed anything in a J Neuro article that I've read in the past few years that reminded me of this policy shift one way or the other.

How about you, Dear Reader? Noticed any changes that appear to be related to this banning of Supplemental Materials?

For that matter, has the banning of Supplemental Materials altered your perception of the science that is published in that journal?

44 responses so far

Chapeau

Occasionally you notice one of your colleagues pulling off something you hope for within your own group.

When your manuscript gets rejected from one journal you would typically submit it to an approximately equal* journal next, hoping to get a more favorable mix of AE and reviewers.

If you've worked up more data that could conceivable fit with the rejected set, maybe you would submit upward, trying a journal with a better reputation.

What is slightly less-usual is taking the same manuscript, essentially unrevised and submitting it to a journal of better reputation or JIF or whathave you.

Getting that self-same manuscript accepted, essentially unchanged, is a big win.

Chapaeau, my friends.

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*You do this, right?

13 responses so far

I really need to start one of these citation cartels....

From Odyssey:

It's become apparent to me that there is a group of reviewers who all display the same phenotype when it comes to their reviews. They all i) are quick to agree to review manuscripts in our common sub-sub-field, ii) submit their reviews on time, and iii) will recommend acceptance or minor revisions for all manuscripts. All.

 

On time? Suspicious that.

Did I mention that this bloc of reviewers are all strongly linked to one particular well-known member of our sub-sub-field? Former trainees, co-authors etc.

 

siiigh.

 

 

 

No responses yet

H-index

I can't think of a time when seeing someone's h-index created a discordant view of their impact. Or for that matter when reviewing someones annual cites was surprising.

I just think the Gestalt impression you generate about a scientist is going to correlate with most quantification measures.

Unless there are weird outliers I suppose. But is there is something peculiar about a given scientist's publications that skews one particular measure of awesomeness....wouldn't someone being presented that measure discount accordingly?

Like if a h-index was boosted by a host of middle author contributions to a much more highly cited domain than the one most people associate you with? That sort of thing.

36 responses so far

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

The "whole point" of Supplementary Data

Dec 10 2014 Published by under Impact Factor, Scientific Publication

Our good blog friend DJMH offered up the following on a post by Odyssey:
Because the whole point of supplemental material is that the publisher doesn't want to spend a dime supporting it

This is nonsense. This is not "the whole point". This is peripheral to the real point.

In point of fact, the real reason GlamourMags demand endless amounts of supplementary data is to squeeze out the competition journals. They do this by denying those other journals the data that would otherwise be offered up as additional publications. Don't believe it? Take a look through some issues of Science and Nature from the late 1960s through maybe the mid 1970s. The research publications were barely Brief Communications. A single figure, maybe two. And no associated "Supplemental Materials", either. And then, if you are clever, you will find the real paper that was subsequently published in a totally different journal. A real journal. With all of the meat of the study that was promised by the teaser in the Glam Mag fleshed out.

Glamour wised up and figured out that with the "Supplementary Materials" scam they can lock up the data that used to be put in another journal. This has the effect of both damping citations of that specific material and collecting what citations there are to themselves. All without having to treble or quadruple the size of their print journal.

Nice little scam to increase their Journal Impact Factor distance from the competition.

19 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

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