Archive for the 'Neuroscience' category

More Neuroscience Smack


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.

*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.

29 responses so far

My new favorite neuroscience smack

May 16 2016 Published by under Neuroscience, Psychology, Society for Neuroscience

22 responses so far

What is "neuroscience"?

At the end of December when everyone was out of the lab on vacation the Journal of Neuroscience twitterers ran an episode of Ask Me Anything, Neuroscience. I had responded to an earlier teaser on this and asked the acting Editor in Chief of the Journal of Neuroscience the question which titles this post, figuring she should know. Obviously, I shaded the question....a little.

She replied:

..which is fascinatingly imprecise. Particularly for an EIC who has to decide categorically what is and is not appropriate material for the Journal she Edits. If we were talking about the range of investigation covered by the presentations at the annual meeting of the Society for Neuroscience, this would be a great answer. The breadth of science at that meeting is tremendous and I can buy that it covers almost everything "to do with neurons". This is not the case for the Journal of Neuroscience. Which should probably be re-named the "Journal of Some Neuroscience but not other Neuroscience".

As you will recall, Dear Reader, I have observed on more than one occasion that as a wee graduate student trainee I realized this fact with some dismay. I was outraged! How can this type of science be okay and this other type of science not, when the only difference is the techniques involved?!??, I wondered. How can these people not see that the Emperor's New Clothes are not better, more precise or more mechanistically insightful results, they are just different levels of analysis?

Over the *cough*cough*decades this attitude has turned to bemusement, particularly as the Journal of Neuroscience's JIF has slid inexorably* down (currently 6.3) into just-barely-above-the-herd levels (25th in the Neuroscience category). Just ahead of such titles as Glia and Brain Behavior and Immunity. It is behind the Journal of Pineal Research, ffs! Yes, yes, JNeuro still punches above its JIF in reputational terms with the cognoscenti but there are many JIF-equivalent-or-better journal options. And after all, we all realize that the JIF still rules where it counts- when people aren't assessing the science from an informed perspective. So the cost to those who do that other type of science involving neurons that is not acceptable for JNeuro has lessened considerably. The gains of sneaking one into the JNeuro have likewise lessened. Better to try at a less technique-limited venue that has a higher JIF

There was followup from the JNeuro twitter intern:

and a related reply from the acting EIC.

Also particularly amusing given the place that "shows mechanism" holds in the mind of the average bio-scientist type, most certainly including neuroscientists, these days. I'd like to see an accounting of how many J Neuro articles in a given year reasonably qualify as "New observation without mechanism". I'm betting the number is so low as to falsify this claim in any reasonable mind.

Then later there was this claim during an unrelated exchange:

Which I think is bizarre buck-passing for an Editor or Associate Editor of a Journal to engage in. At the least, it illustrates how and why it is bogus to claim "New observation without mechanism" is welcome-- if one only selects reviewers who will not buy this for a second then where are we? Also, I am curious if AEs use the presumption of what reviewers might say to desk-reject said manuscripts. See also, the above comments about what qualifies as "neuroscience" and whether or not certain approaches and techniques are ruled in/out at this particular journal. Speaking as a reviewer, I try to follow the Editorial lead in the sense that "appropriate for this journal" has to be recommended, I rely on what they have actually been publishing**.

In closing, I'll point out that I write this for the current version of younger-me. Those of you who aspire some day to publish in J Neuro, because you are a proud neuroscientist and proud member of the Society for Neuroscience. You who bring your posters to the Annual Meeting and then notice, chillingly, that science like yours never seems*** to get published in J Neuro. Have a heart. Leave your Imposter Syndrome behind. There are many so-called "more specialized" (that's meant to be an insult when reviewers or AEs say that, btw) journals which have better JIFs. Get your work published there. Keep coming to the SfN meeting and chatting with the folks who appreciate what you do.

Keep on with the science that satisfies you.

And feel free to snicker about those people who do cell biology accidentally in neurons and call themselves neuroscientists.

*all snark aside, I do lament this. J Neuroscience is a great journal and resisted Glamming it up and JIF chasing in response to the invention of Neuron and Nature Neuroscience. It is unfortunate it is being punished for this. And of course, before the aforementioned baby Glams, it really did shine as a pinnacle for a Society published journal.

**Unless, of course, I am engaging in a rather intentional pushback along the lines of what the JNeuro EIC is suggesting, i.e., putting my marker down that I think the journal in question should be publishing a certain kind of paper.

***Yes, there will be the occasional paper that gets into a given journal. And you will think "aha, we have something very similar so let's submit!". Give it a try for sure. But don't be too amped when you get desk-rejected. Often enough you will find out that the relationships between the editorial staff and the authors is slightly closer than you enjoy. Shrug and move on. Or, if a PI and you DGAF about your reputation at that particular journal, write a pointed inquiry to the AE to see what they say. I had one of these at a journal that rhymes with Serebral Kortex awhile ago. The new editorial staff tried to slam the old editorial staff and basically said, well that would never get in anymore. I was amused. And we published that paper somewhere else and moved on. As one does.

42 responses so far

SFN 2015: What are the socials for?

The SFN Annual Meeting is famous for the overwhelming barrage of science being fire-hosed at you. It is intimidating and can be impersonal.

Almost equally famous, particularly for the experienced hands, are the evening thematic socials. These are gatherings that may be focused on a scientific topic (Dopamine), University, lab (for the big ones), academic society (yes, the competition comes to SFN to troll for members) and/or organized by vendors (such as a journal/publisher).

Here is a list of the things I accomplished at one social this year:

-Talked with a colleague from whom I requested an emergency grant support letter just prior to the meeting. I explained the wheres/whys and thanked her profusely.

-Chatted with a colleague who is in semi-competition with one of our research domains. We worked some stuff out, talked a little about plans and I hope pre-empted what could have been bad feelings on one side or another.

-I met a junior scientist (that I didn't know except second hand) who had asked me for a letter of support for a grant application on the recommendation of a PO. This person told me more about the project and I was able to comment on a few things.

-Met a philanthropist who donated to a lab in which I have an interest. I kid you not.

-Chatted with a more-senior member of my field who is of pretty high stature in a subfield. I would not necessarily have gotten to know this investigator absent this particular SFN social over the past couple of years. This PI commented about my research directions in a thoughtful way that shows she actually knows me beyond social recognition.

-Met a postdoc who is nearing the job market in a subfield in which I have slightly better than average ear-tuning about job openings. I will be able to forward things that I hear about to this person now.

That's off the top of my head. I am sure there were several less-obviously work-related conversations that in fact have a work-related component to them.

So there are two points.

First, when you hear people talking about this or that fantastic party they attended at SFN, remember that these socials are there for work and career related purposes.

Second, the party that I am referring to was BANTER, organized by Scientopia's very own Dr Becca over the past five or six years. The organizing theme is not any of the usual one that you might think of as being specific to your career interests. It is based on the online science community, most especially the Twitter-based neuroscience community. It is not screened for any particular subdomain of neuroscience, including mine, and yet I had the above-mentioned interactions.

The implication* of this latter observation is that you can engage in useful work-related conversations at almost any SFN social, which means that it can be less forced. Go to the ones where you have the most interest, or an "in" or whatever. The key is to

*I think it also points to how firmly BANTER has become implanted on the SFN social map. Well done Dr Becca, well done.

41 responses so far

Ask Drugmonkey: Call to the Hivemind on Behavioral Neuroscience coursework

A longtime Reader asks:

My colleagues and I are trying to finalize our revisions/updates to the courses we will require as part of a PhD in behavioral neuroscience. It would be helpful to get input on what others' experience is: how many credit hours of classwork are required, and what are seen as the essential items? [We're at 47 class credits currently, trying to reduce to either 41 or 38 but facing resistance to eliminating non-neuro psychology classes from requirements.]

Anyone have any thoughts on this?

I myself think that "eliminating non-neuro psychology classes" is a huge mistake and I join their local resistance. The field of so-called behavioral neuroscience already has far too many people who are insufficiently grounded in good old Behavioral Psychology.

If you take the current replication hoopla seriously, it is a bad idea to cut behavior out of the curriculum.

31 responses so far

Tracking sex bias in neuroscience conferences

Aug 31 2015 Published by under Careerism, Conduct of Science, Neuroscience

A Tweep directed my attention to of which the About page says:

The progress of science is best served when conferences include a panel of speakers that is representative of the field. Male-dominated conference programs are generally not representing their field, missing out on important scientific findings, and are one important factor contributing to the “brain-drain” of talented female scientists from the scientific workforce. As a group, BiasWatchNeuro has formed to encourage conference organizers to make every effort to have their program reflect the composition of their field.

Send information about conferences, seminar series or other scientific programs to

Check it out.

43 responses so far

Logothetis driven out of monkey research

May 04 2015 Published by under Animals in Research, Neuroscience, Science Politics

Neuroscientist Nikos Logothetis (PubMed) has informed his colleagues that he is stopping his long running nonhuman primate research program. An article in ScienceInsider by Gretchen Vogel details the issues:

Nikos Logothetis, a director at the Max Planck Institute for Biological Cybernetics in Tübingen, Germany, says he will conclude his current experiments on macaques “as quickly as possible” and then shift his research to rodent neural networks. In a letter last week to fellow primate researchers, Logothetis cites a lack of support from colleagues and the wider scientific community as key factors in his decision.

This is not the "start" as was alleged by a Twitter person today. This is a long running trend that has been going on for decades. Productive laboratories that use nonhuman primates have been closing one by one. The decision by Harvard to shutter the New England National Primate Research Center was shocking in the way it violated the trend for picking off research labs one by one, but it was otherwise simply part of a larger trend.

And why are Universities and Research Institutes like Max Planck divesting themselves of monkey labs as quickly as possible? The Vogel article suggests an answer.

Logothetis’s research on the neural mechanisms of perception and object recognition has used rhesus macaques with electrode probes implanted in their brains. The work was the subject of a broadcast on German national television in September that showed footage filmed by an undercover animal rights activist working at the institute. The video purported to show animals being mistreated.

Logothetis has said the footage is inaccurate, presenting a rare emergency situation following surgery as typical and showing stress behaviors deliberately prompted by the undercover caregiver. ... The broadcast triggered protests, however, and it prompted several investigations of animal care practices at the institute. Investigations by the Max Planck Society and animal protection authorities in the state of Baden-Württemberg found no serious violations of animal care rules.

Emphasis added. This is a typical scenario. In essence, animal rights terrorist fanatics are able to get Universities and Research Institutions to turn their backs on productive researchers simply because they don't want to deal with the headaches any longer. Or because they fear bad press. The accusations are almost always falsified. Baseless. But it doesn't matter. The Universities are running in absolute terror of the fanatics.

Of course it goes beyond that, which is why Logothetis called out his fellow scientists.

The [Max Planck] society is “one of the best scientific organizations worldwide,” Logothetis wrote, but it has failed to take concrete steps against the activists. “I am no longer willing or able to accept the never-ending stream of abuse from animal activists toward myself and my co-workers while seeing them encouraged to increase their aggressive activities by the tolerance and very slow reactions of scientific organizations. There is a clear lack of consequences for illegal actions such as infiltration, violation of privacy, theft of documents, and even intentionally caused distress to animals in order to film supposed animal torture or abnormal behavior,” the letter states.

Logothetis’s letter also faults his scientific colleagues in Tübingen for distancing themselves from the controversy. The neighboring Max Planck Institute for Developmental Biology posted a disclaimer on its website emphasizing that there are no monkeys at the institute, he notes, and colleagues at the nearby Hertie Institute for Clinical Brain Research refused to issue a declaration of support.

Pastor Niemöller once observed:

First they came for the Socialists, and I did not speak out—
Because I was not a Socialist.

Then they came for the Trade Unionists, and I did not speak out—
Because I was not a Trade Unionist.

Then they came for the Jews, and I did not speak out—
Because I was not a Jew.

Then they came for me—and there was no one left to speak for me.

There are certainly parallels. Biological scientists express a range of attitudes about many things and the use of animals in research is one of them. From fears of coming under assault themselves if they speak up, to discomfort with making an informed decision about the allegations against Professor Logothetis to frank antipathy to research in monkeys, we span the same range as many lay people.

We are easily able to delude ourselves that if we just let the most-detested targets of the terrorists get thrown under the bus, we can live our own lives in relative safety for another few years. Maybe run out the clock on our career before things get too bad.

Money is tight, after all, and gee, well lets not do anything to rile up the nice little old ladies who are poised to donate a few million to the University, eh? Let's not do anything to draw the attention of animal right's Congress Critters. That might make things awkward for the NIH.

Normally this is the point of my post where I exhort you to fight. To stand up and oppose this assault on scientific research. Where I point out to you that after the monkeys (and cats and dogs) comes the goats and the rabbits from which you get your antibodies. Where I tell you that all this pressure is doing is to move certain kinds of research to non-Western countries in which the animal research protections are, at best, at the lever of the US in 1950.

This is the point where I am supposed to be telling you to call your Congress Critter.

But I can't.

Logothetis is not the first and he will not be the last.

We have had ample opportunity for biological scientists to see and be motivated to do something about this situation.

They have not done so.

So I would be wasting my breath.

43 responses so far

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.
*BTW, a Nature editor confirms this microscopic incremental advance is what is new about this paper.

66 responses so far

Sometimes the good guys win

Sep 30 2014 Published by under Neuroscience, NIH

I've mentioned a time or two that I think the DREADD approach is infinitely more useful than optogenetics for anything that matters.

So congrats to the team for this new award.


DESCRIPTION (provided by applicant): The Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative has the ambitious goal of elucidating how neuronal ensembles interactively encode higher brain processes. To accomplish this goal, new and improved methods for both recording and manipulating neuronal activity will be needed. In this application, we focus on technologies for manipulating neuronal activity. The major significance of this application is that we will provide an enhanced chemogenetic toolbox that allows non-invasive, multiplexed spatiotemporal control of neuronal activity in domains ranging from single synapses to ensembles of neurons. To achieve this, we will provide: Chemical actuators with improved pharmacokinetics and pharmacodyamics suited for use with current DREADDs in eukaryotes ranging from Drosophila to primates (Specific Aim #1) Photo-caged CNO and other chemical actuators to provide millisecond-scale control (Specific Aim #1) Novel DREADDs and 'split-DREADDs' targeted to distinct neuronal pathways to enable multiplexed interrogation of neuronal circuits (Specific Aims #2 and 3) Chemogenetic platforms with minimized desensitization and down-regulation (Specific Aim #3)

I am excited to see where this leads.

More awards under The BRAIN Initiative.

27 responses so far

Hard truths for supposed neuroscientists

This is the truest and best thing I have read on the internet today.

12 responses so far

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