Papers

(by drugmonkey) Jan 21 2016

January is a great time to look at yourself in the mirror and ask what your plan is for improving your record of publication.

What are your usual hurdles that get in the way? What are the current hurdles?

What works to get you moving?

My biggest problem is me.

We're at the point in my lab where available data are not really the issue, we have many dishes cooking along in parallel at most times. Something is always ready or close to being ready to serve up.

The problem is almost always the wandering of my attention and my energy to kick something over the final step to submission.

The game I have taken to playing with myself is to see how long I can go with at least one manuscript under review. I made it something like 14 mo a few years ago. Of course I then promptly fell into another extended dry spell but....

The other game I play with myself is to see how many manuscripts we can have under review simultaneously. That is, of course, much more subject to the ebb and flow of project maturation and the review process. But if we happen to have a few stacking up, sure I'll use the extra motivation to keep my attention pegged to finishing a draft.

When all else fails there is always "We need this published in order to help get this next grant funded, aiieeeee!"

39 responses so far

Where will your lab be in 5 years?

(by drugmonkey) Jan 12 2016

Scientifically, that is.

I like the answer Zoe gave for her own question.

I, too, just hope to be viable as a grant funded research laboratory. I have my desires but my confidence in realizing my goals is sharply limited by the fact I cannot count on funding.

Edited to add:

When I was a brand new Assistant Professor I once attended a career stage talk of a senior scientist in my field. It wasn't an Emeritus wrap-up but it was certainly later career. The sort of thing where you expect a broad sweeping presentation of decades of work focused around a fairly cohesive theme.

The talk was "here's the latest cool finding from our lab". I was.....appalled. I looked over this scientist's publication record and grant funding history and saw that it was....scattered. I don't want to say it was all over the place, and there were certain thematic elements that persisted. But this was when I was still dreaming of a Grande Arc for my laboratory. The presentation was distinctly not that.

And I thought "I will be so disappointed in myself if I reach that stage of my career and can only give that talk".

I am here to tell you people, I am definitely headed in that direction at the moment. I think I can probably tell a slightly more cohesive story but it isn't far away.

I AM disappointed. In myself.

And of course in the system, to the extent that I think it has failed to support my "continuous Grande Arc Eleventy" plans for my research career.

But this is STUPID. There is no justifiable reason for me to think that the Grande Arc is any better than just doing a good job with each project, 5 years of funding at a time.

137 responses so far

Top Powerball winner fantasy (of academic scientists)

(by drugmonkey) Jan 11 2016

"If I win the Powerball, I can afford all kinds of new domestic help and maybe even figure out how to issue grants to my lab so that I can spend more time publishing papers."

37 responses so far

Top one of one Powerball winner fantasy (of most people)

(by drugmonkey) Jan 11 2016

One response so far

Minions

(by drugmonkey) Jan 08 2016

I don't care what stage of the doctoral arc you inhabit, having science minions helps move your science forward.

The more minions, the better, assuming you have the resources available to fill their time productively.

If you don't want moar data than you can generate with your own two hands, this is not the right career for you.

53 responses so far

I'm 14 carat......want to look good for the PI, mmm

(by drugmonkey) Jan 06 2016

Have you ever been in a lab with a golden-child trainee?

Was it you?

61 responses so far

What is "neuroscience"?

(by drugmonkey) Jan 05 2016

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

What is a scientific "observation"?

(by drugmonkey) Jan 05 2016

Reference to this https://t.co/hc9YYH8Myr popped up on the Twitter recently.
So what constitutes an "observation" to you?

To me, I think I'd need the usual minimum group size, say N=8, and at least two conditions or treatments to compare to each other. This could be either a between-groups or within-subject design.

22 responses so far

Dissection of sleazy, dishonest AR shillery posing as journalism

(by drugmonkey) Jan 04 2016

Notice what I did there? Setting a bias right from the start with click-bait headlining?

Well, that is just how a buzzfeed piece entitled "The Silent Monkey Victims Of The War On Terror" starts.

"Victims".

I called this piece out for being sleazy and dishonest in a tweet and the author, one Peter Aldhous, Buzzfeed News Reporter, took exception. He emailed me asking how I could possibly accuse him of being a shill for the AR agenda, asserting he has no allegiance whatsoever to animal rights and complaining about how someone as allegedly influential as me could damage his professional reputation.

So I felt I owed him an explanation.

First, I make no apology for my distaste for AR adherents. They are terrorists, yes, terrorists, and they inhabit a nihilist, anti-social ideology. Of terrorism.

Second, I've written a few posts about the use of animals in research (see below for Additional Reading). There is a pretty good dose of information at Speaking of Research as well. I mention this not so much to draw specifics as to show that there is information available on the web, readily searchable, for a journalist to quickly find for an alternative viewpoint to the AR nonsense. That is, if they are interested in researching a story. I'll also point out that the Science Editor at Buzzfeed is someone who spent years pounding the floors at the annual meeting of the Society for Neuroscience and has even written on the use of nonhuman primates in autism models. Again, the point is that this journalist has a route to further education and balance, if he had only chosen to use it. The piece does not reflect any such background, in my reading of it.

What I want to dissect today, however, is the way this piece by Aldhous is carefully crafted to attack nonhuman primate research, as opposed to providing a reasonable discussion of the use of animals in specific research.

The article starts with "victims" and has chosen to describe this as resulting from "The War on Terror". Right away, we see a sleazy link between something that many Americans oppose, i.e., the description of the Bush agenda as a war on terror and the Bush agenda itself, and the use of animals in research. It is a typical tactic of the AR position. If you can establish that one area of research is unneeded in the eyes of your audience then you are three quarters of the way home.

And this is AR thinking, make no bones about it. Why? Follow the logic. There are sizable swaths of Americans who disagree that we should spend public money investigating any number of health conditions. From infectious disease like HIV (although see this) to obesity to diabetes to depression to substance abuse. Simply because they do not agree that these are topics that are worth of investigation. Anthrax, botulism and nerve gas are no different in this respect. Some people feel that the war on terror is overblown, the risks of a bio or chemo weapon attack are small and we should not put any public money into this topic whatsoever- from research to law enforcement.

So if you argue that your particular agenda should rule the day when it comes to research, you are saying that everyone's agenda in a pluralistic democratic society should rule the day. This leaves us with very little science conducted and certainly no animal science. This is why I call this a bit of AR shillery. The logic leads to no animal research on any health topic.

Note, it is fine to hold that belief in pluralistic democratic society but let us be honest about what you are about, eh? And sure, I can see that there would be some agenda so narrowly focused, so out of the mainstream that we cannot reasonable credit as being a legitimate concern of the American people. It should be self-evident from the support for the Bush administration's war on terror (and our public discussion over bioterror) that this is not the case here.

Ok. But what about the converse? Is just any use of animals in research okay then? No, no it is not. Certainly, we have a cascade of federal law, federal regulation and widely adopted guidelines of behavior. We have rules against unnecessary duplication. We wrangle, sometimes at long length, over reduction and refinement of the research that uses animals. Even an apparent exemption from the full weight of the Animal Welfare Act for certain experimental species doesn't really exempt them from oversight.

Getting back to the article, it next pursues two themes including the idea that there are a "lot" of monkeys being used and that they are all "suffering" and in pain. The article includes this pull quote:

“Wow, that’s a lot of monkeys,” said Joanne Zurlo of the Johns Hopkins Bloomberg School of Public Health, who studies alternatives to animal experimentation. “It’s quite disturbing.”

It is? How do we know this? How are we to evaluate this with any sort of context? How is it "disturbing" unless we have already decided we are against the use of monkeys in this, or for that matter any, research?

The piece brags about some exclusive review Buzzfeed has conducted to examine the publicly-available documents showing about 800 nonhuman primates used in "Column E" (the most painful/distressful category) US research in the 1999-2006 interval and a jump to about 1400 in the 2009-2014 interval.

Speaking of Research maintains an animal-use statistics page. The US page shows that of the species not exempted from tracking by the Helms Amendment, non-human primates account for 7% of the total (all categories of research use) in 2014. This is 57,735 individuals- note that given that non-human primates can be used for years if not decades in some kinds of research, this does not equate to a per-year number the way it would for a species that only lives 2 years like a rat. But at any rate, the 600 extra [ETA: "E" category monkeys] that the Buzzfeed piece seems to be charging to the war on terror is only a 1% increase in the annual "E" use of non-human primates.

This is "disturbing"? Again, I think this alone shows how disingenuous the piece really was. A "one percent increase in the use of monkeys for bioweapon research" doesn't really have the same punch, does it?

What about other frames of reference? From the Speaking of Research page:

Scientists in the US use approximately 12-25 million animals in research, of which only less than 1 million are not rats, mice, birds or fish. We use fewer animals in research than the number of ducks eaten per year in this country. We consume over 1800 times the number of pigs than the number used in research. We eat over 340 chickens for each animal used in a research facility, and almost 9,000 chickens for every animal used in research covered by the Animal Welfare Act. For every animal used in research, it is estimated that 14 more are killed on our roads.

Or what about the fact that Malaysia culled 97,119 macaque monkeys (long-tailed, i.e. M. fascicularis and pig-tailed, i.e. M. nemestrina; common research lab species) in 2013. Culled. That means killed, by rough means (by the reporting) without any humane control of pain or suffering. No use for them, no scientific advances, no increase in knowledge...probably not even used for food. Just.....killed. 167 times the number scored as used in bioweapons research were just eliminated in a single year in a single country.

Failing to provide these contexts, and writing a piece that is majorly focused on the number of research monkeys used for bioweapons studies is dishonest, in my view.

Okay, so what about the pain and suffering part of the piece? Well, Aldhous writes:

BuzzFeed News has calculated the number of primates used each year for what the USDA calls “Column E” experiments, in which animals experience pain or distress that is not fully alleviated with painkillers, tranquilizers, or other drugs. Because monkeys are emotionally complex creatures that are thought to experience suffering similarly to how we do, such experiments are especially controversial.

The number of primates used in these ethically fraught experiments

Notice the slant? First of all, human introspection about the "pain and suffering" of nonhumans is suspect, to say the least. Yes, including monkeys, dolphins or whathaveyou. The statement about monkeys being "emotionally complex creatures" is pure AR theology. The idea that nonhuman suffering is identical to human suffering is entirely unproven and there are large numbers of people who disagree with this characterization (see the Malaysian culling, above, for an example). If you try to get people to define terms and provide evidence you devolve into really bad eye-of-the-beholder anecdata on the one hand up against a profound lack of evidence on the other. Humans are demonstrably different from all other species we know to date. And efforts to view nonhumans as "like us" invariably involve some very convenient definitions, goal post moving, blindness to the quality or universality or ease of the human trait, etc.

Calling it "especially controversial" and "ethically fraught" is hardly even handed journalism. Where is the balance here? The people who shout loudest about the use of monkeys being "controversial" don't believe in any animal research. Seriously, probe them. What use of animals isn't ethically fraught? Hammering this idea over and over throughout the piece is poisoning the well. It is acting like this is established fact that everyone agrees with. Not so. And the slant of these terms is certainly on the side of "this research is bad". You use other terms when you want to describe a neutral disagreement of sides.

One very important point is the lie of the truncated distribution. We know perfectly well that there is a big part of the American distribution that is essentially unconcerned about animal use and animal suffering. If you know anyone who uses sticky traps to deal with unwanted household rodents...they are doing Category E research. Catch and release fishing? Ditto. People who own large dogs in city apartments and walk them just twice a day....well it isn't Category E but it sure doesn't sound humane to me. The point is that research and researchers do not operate in this part of the distribution. They operate in the well-regulated part of the distribution that is explicitly concerned with the welfare of animal subjects in research. Notice all the pull quotes he included from researchers seem to express caution? Obviously I can't know how selected and cherry picked those comments were (I suspect very) but they do testify to the type of caution expressed by most, if not all, animal researchers. We are always looking to reduce and refine. And look, individual scientists may view different research priorities differently...but it is hardly fair to only present the skeptics. Where are the full throated defenders of the bioweapons research in this article? Well, they wouldn't talk on record* due in very large part, I assert, to a well-informed skepticism that journalists ever care to be balanced on these topics.

The Aldhous piece goes on to a very sleazy sleight of hand by mentioning a violation report in which an animal research facility was cited for failing to follow care protocols. He picks out three institutions:

three institutes have dominated the most ethically contentious primate experiments: the U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID) at Fort Detrick, Maryland, the Lovelace Respiratory Research Institute in Albuquerque, New Mexico, and the Battelle Memorial Institute in Columbus, Ohio.

Since 2002, these three institutions have collectively used more than 6,400 Column E primates. In 2014, they accounted for almost two-thirds of the monkeys used in these experiments.

Again with the "most ethically contentious" charge. Nice. But the point of this is...what? Many bioweapons pathogens can only be studied at very high cost isolation facilities. It is good and right that there are not many of them and that they account for the majority of the animal use. It is also good and right that they are subject to regulatory oversight in case any slip ups need to be corrected, yes?

After a routine inspection in March, Lovelace was cited for failing to provide monkeys with the care that was supposed to be delivered — including intravenous fluids, Tylenol for fever, and antidiarrheal drugs.

The report shows that three animals did not receive Tylenol when they should have, and three did not receive anti-diarrheals when they should have, for 2-4 days of symptoms. There were 57 animals in a Cohort that did not receive injections of fluids but there is no indication that this resulted in any additional pain or distress and we can't even tell from this brief protocol language whether this was supposed to be as-need-per-veterinarian-recommendation or not. There are two additional Cohorts mentioned for which it is noted the animals were treated according to protocol and the table in the Aldhous piece lists 431 animals used at Lovelace in 2014, probably the year for which the above citation refers. Naturally, Aldhous fails to mention these citation numbers leaving the reader free to assume the worst. This is classic misdirection and smearing at work. Which is why I call it dishonest. "Loose stools or fever for 2 to 4 days in less than 1% of individuals" sounds more like an over the counter medication warning or a threshold for when to finally call the doctor to the average ear.

Aldhous next diverts into a fairly decent discussion of how animal models may or may not fully predict human outcome but I think that in the context, and with his shading, it falls short of the mark. I'm not going to step through all of his examples because there are certain fundamental truths about research.

1) If we knew the result in advance, the experiments wouldn't be necessary. So if we sometimes find out that animal models are limited, we only come to this conclusion in the doing. There is no way to short circuit this process.

2) We use animals, even monkeys, as proxies and models. Sometimes, they are going to come up short of full prediction for human health. This does not mean they are not valuable to use as models. Again, see 1. We only find this out in the doing and most research is novel territory.

3) The overlap between animal testing and research is fuzzy in this discussion. If you want to evaluate medications, your research may not be dedicated to, or idealized for, novel discovery about the disease process itself. This doesn't make it less valuable. Both have purposes.

4) It is dishonest to point to places where animal research failed to predict some adverse outcome of a medication in humans without discussing the many-X more potential medications that were screened out with animal models. Protection from harm is just as important, maybe more so, than identification of a helpful medication, is it not?

So as you can see, I think this piece in Buzzfeed is written from start to finish to advance the AR agenda. It is not by any means fair or balanced. This is relatively common with journalism but that is no excuse. It is sleazy. It is dishonest. There is every reason to expect that balanced information and opinion is readily available to a journalist, even one who has no scientific background whatever.

I do not know the heart and mind of the author and as I mentioned at the outset, he protested vehemently that my take was not his intent. Which is why I have tried to focus on the piece and what was included and written. I will suggest that if Aldhous is sincere, he will read what I have written here, follow the links and take a very hard editor's look at what he has written and the impact it has on the average reader.

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*I don't know the solution to this problem. A piece like this one Aldhous wrote is the type of thing that hardens attitudes. Which makes it harder for the balanced story to get out. It's a vicious cycle and I have no idea how to break it until and unless science journalists stop with this sleazy and biased AR shillery on their own.

Additional Reading

Logothetis driven out of monkey research

UCLA scientists have been under attack for over a decade

Repost: Insightful Animal Behavior: A "Sufficiently Advanced Technology"

Dolphins ain't all that either

33 responses so far

Aphorism

(by drugmonkey) Jan 02 2016

Found this on the Facebooks. It seems appropriate for a science-careers audience:

There was a farmer who grew excellent quality corn. Every year he won the award for the best grown corn. One year a newspaper reporter interviewed him and learned something interesting about how he grew it. The reporter discovered that the farmer shared his seed corn with his neighbors. “How can you afford to share your best seed corn with your neighbors when they are entering corn in competition with yours each year?” the reporter asked.

“Why sir,” said the farmer, “Didn’t you know? The wind picks up pollen from the ripening corn and swirls it from field to field. If my neighbors grow inferior corn, cross-pollination will steadily degrade the quality of my corn. If I am to grow good corn, I must help my neighbors grow good corn.”

11 responses so far

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