COPE: Nothing more than a useless trade association

I’ve said it before and I’ll say it again – COPE (the Committee on Publication Ethics) is nothing more than a trade association / lobby group for the publishing industry.  Its real job is to provide a feel-good excuse for the multi-$bn publishing industry to say “hey look we’re doing something about ethics”, in return for subscription fees. In the same way that being listed in Who’s Who appeals to vain individuals, being listed as a COPE member buys journals a semblance of ethical credibility.

What if that credibility counts for nothing?  As reported yesterday by Neuroskeptic, a new study by Morten Oksvold found a shockingly low rate of response from journal editors when confronted with blatant evidence of data irregularities in over 40 papers spread across 3 journals.  The response rate?  Zero. Zilch. Nada. Niente. Nil.

Guess what? All 3 journals are COPE members! The COPE Code of Conduct specifically tells editors to respond stating what they plan to do in such cases. Ignoring such communications is a definite no no.

From my own experiences, this is a common outcome.  Just about every journal or major publisher is a member of COPE, and yet time-and-again we see COPE guidelines being openly flouted. In one of the cases listed in that post (J. Neurosci. paper) I’ve been waiting over 2 years for the publisher to get their proverbial feces together. Last fall the case was raised to the level of a formal investigation by the ethics committee of the Society for Neuroscience, but they’ve stopped responding to my emails, despite me CC’ing COPE. The burden for ensuring that alleged data problems are dealt with in a timely manner falls firmly at the feet of the journals and their so-called trade association. It should not require Herculean efforts on the part of bloggers.  We know how to do this stuff properly – it just requires lazy editors to do their damn jobs!

What are the consequences for a journal or editor, if a breach of the COPE guidelines occurs?  Well, based on the Cell case I outlined in that previous post, there were none. The editor still has her job. There was no formal public announcement that the COPE guidelines had been breached. No indication that the person or persons behind the blatant conflict-of-interest suffered any negative effects whatsoever. A simple email to me (the complainant) stating that “procedures will be reviewed and improved”, and we all move on pretending this is fixed, and won’t happen again.

The underlying issue here is that COPE doesn’t have any teeth. All of the power is held by the journals, and COPE is their obedient little lap dog. When journals screw up, COPE could threaten to rescind their membership, but who in their right mind is going to challenge a multi-$bn giant such as Elsevier?

As scientists, we need to be frank about the reality of the relationship between the publishing industry and COPE.  If we want ethics cases to be handled properly, squealing to a pay-to-play vanity club is not the answer. COPE has consistently proven that they don’t have the power to change deeply entrenched behavior by editors. In contrast, taking matters into our own hands by using social media and sites such as PubPeer, continues to be an effective strategy to get results.

University admin’ run amok (this time it’s IT)

It’s been a while since I wrote about the ridiculous administrative burden that is gradually sucking. the. will. to. live. of everyone in academia.  Today I want to focus on a specific example… what happens when the IT people take a reasonably simple task, and strangle it the complete fuck to death?

It starts out with a relatively simple problem… we use animals in my lab’,  so we’re required to have animal protocols in place. The body administering these protocols is called UCAR – the University Committee on Animal Resources [Fun fact – it’s almost always called IACUC at other institutions, but our UCAR is actually one of the oldest, so its been around since well before that naming trend emerged].

One of my animal protocols is up for annual renewal – a simple series of 3 questions that could be handled in a 30 second email – Is the protocol still active? Has anything changed since last year?  How many animals have been bred and used since the last renewal?  There’s a far more comprehensive review process every 3 years, or if you need to change/add anything, but so long as you’re just trucking along and everything is in compliance then the annual protocol renewal is as close as it gets to a rubber stamp affair – until the IT department gets involved…

UCAR has a simply wonderful (!) online interface for dealing with submission and processing of protocols. It’s called TOPAZ – but don’t click that link in Firefox because it will crash your browser, even if you have the correct Silverlight plug-in installed!  One time, TOPAZ went down “for weekend maintenance”, and when it came back on-line the following Thursday, all the menus were in German. The site can best be described as a total clusterfuck – pasting text in there from other documents causes huge formatting problems; menu scrolling is a disaster; navigation to utterly counter-intuitive. All really simple “web design 101” stuff, but when you have a virtual monopoly on this sort of product, you don’t have to give a shit about the customer experience!

But today that’s not the problem.  Oh no, today I had to spend 15 minutes trying to find the frickin’ link to TOPAZ (yeah yeah I should have it bookmarked, but I just replaced my computer and didn’t migrate everything yet).  Anyway…

The Website Overhaul
Until recently, there used to be a simple web interface at URMC, but recently the IT folks have been overhauling everything. Something to do with branding and other concepts way above my pay grade. As highlighted by this XKCD comic, University websites are renowned for providing zero of the information people actually visit them for.  At URMC, they’ve taken it to a whole ‘nuther level. This is what you see at the main page…
urmc main page grab

That’s a normal size browser window, taking up 2/3 the width of a 1440×900 wide-screen monitor. See any menu bars?  See anything worth clicking if you actually WORK at the place?  No. To get to the good stuff you have to scroll past all the PR bunk to the end of the page…
.urmc main page grab lower

See anything there about resources or other useful links for researchers (such as a link to UCAR?). BOOM!  Of course, how could I have missed it?  See that little thing at the top right of the main page (in the last-but-one image)? That’s a menu link. Someone (probably working on a 21″ iMac) thought it would be a good idea to have the menu options that appear on a regular webpage collapse into a small icon if the browser is below a certain width. If only I’d widened my browser to full screen width, this is what I would have seen at the top of the page…
urmc main page grab wide

OK, let’s follow that “research” link, and go to Resources for Researchers. Nope, nothing there.  What about Shared Resource Laboratories? No, that’s all the core facilities. What about the listing of Departments and Centers?  Well it’s not under U for UCAR. Maybe A for animal? Bingo – Animal Resource, and it has a link to UCAR’s page…
UCAR main page

But is there a link to TOPAZ? No. Maybe it’s in that menu thing over on the top right? No. Oh, but wait, TOPAZ only works with Internet Explorer, let’s fire that up before we get too far down the rabbit hole in FireFox.
ucar in ie

Same deal.  Oh but look, in addition to that menu thing in the top right, there’s a little “+” sign. It wasn’t there in FireFox (see above). Hmm… wonder what that does?
ucar auprot menu

Right there – 4th item down the menu – “Animal Use Protocols”.  Click that, and you get a page describing protocols, but still no link to the submission site!  Oh, but now you’re on the protocol page, go back up to the “+” sign again and click it to expand.. Now there’s a new menu item below Animal Use Protocols… “Submit Protocol Online”  It wasn’t there before.
ucar submit protocol link

OK. Clicking that link brings you to this page, where you can click the link to log into TOPAZ.  If you’re lucky, TOPAZ might launch the first time, or it might crash, but it usually works the second or 3rd time.

Oh but it’s not over yet.
Having wasted my time on this, I decided to file a complaint with web services. (another 5 min. to find the appropriate link, since it’s not listed under any of the obvious headings such as IT or Computing).

As expected, there’s no number to call, no contact email address, just a button to click to File a Support Ticket. That brings up this window, which requires log-in (same user ID as for TOPAZ, which incidentally is the same user ID for email, the HR system, a bunch of other internal sites, plus WiFi access – can you say security risk?)  Anyway, you click “New Ticket” and the browser crashes! Mother fucker!
web services support ticket

Some people question why I run my own lab’ website instead of entrusting it to the institution.  In future I will simply direct them to this blog post.

More super happy fun admin times as a professor…
(1) We’re trying to hire a new post-doc’ who’s on an H1B visa. By last count I’m up to 52 emails between myself, the Office of Postdoctoral Affairs, my Department, and the International Services Office.

(2) We also recently hired a new lab tech’ from another lab’ where the PI is moving away. The logistics of doing this were a total nightmare, including a lovely 45 minute ‘phone call with HR to be briefed on the nuances of NY state labor law. Whether this person will get their first paycheck on time is still up in the air.

(3) A lag in ledger reporting on a soon-to-finish grant, led what was thought to be a $5k surplus in need of urgent spend-down, turning into a $4k deficit in the space of a week. The phrase “it hasn’t hit the ledgers yet” keeps me awake at night.

(4) All the same old crap I wrote about before is still there piling up, getting in the way of my ability to actually DO science.

We all have a duty, as scientists and university faculty, to fight this continual onslaught of administrative BS.  If you haven’t read this book, do so, and get angry.


The end of an era, and the beginning of several new ones…

This spring there have been a lot of changes around the lab…

– Our technician Bill Urciuoli graduated his MBA from the Simon School of Business at UR (tuition benefits FTW), and left us in April to start a new job in Williamsport PA.  We will have a few weeks without a technician (oh joy!) and our new Tech’ will hopefully be starting on June 1.

– Long-term colleague Dr. Chad Galloway has started a new job as a staff scientist in the Department of Ophthalmology here at URMC. Here’s a picture of Bill and Chad at their leaving party – the bucket on the floor is part of a beer brewing kit they each got as a leaving gift.


– We’ve also had an RIT co-op student in the lab’ for the past 3 months.  Nick Gulati has been doing a lot of 3D printing, and we recently obtained some electrically-conductive printer filament from Proto-Pasta, which he’s been using to print custom electrodes (more news on this soon).

– Our multi-PI R01 (with Keith Nehrke from Medicine and Cole Haynes from Sloan Kettering) got funded!  The project is entitled “Role of the mitochondrial UPR in ischemic protection”, and as the name suggests, will seek to characterize the key players in the mitochondrial unfolded protein response, and how activating this pathway might be able to protect the heart from ischemia-reperfusion injury.

– Andrew Wojtovich (former psot-doc’ and now an R.A.P. in the Department of Medicine) got a fundable score on his first R01, entitled “Optogenetic control of mitochondrial ROS generation”. Andrew was also selected to give a talk at the annual Biochemistry Department retreat.

– We were privileged to host Aubrey DeGrey of the SENS research foundation, for a seminar. I’ve known Aubrey since >20 years ago from the UK, so it was great to catch up on old times and hear all about his exciting recent advances in aging research.

– We had a visit from former grad’ student Dr. Lindsay Burwell, who reports that she’s going to start a new position as an Assistant Professor of Chemistry at Wells College this fall.


3D printed gel combs

One of the ideas out there in the “3Dprintosphere”, is that seemingly common plastic doo-dads are way too expensive, and would be a lot cheaper if they could be custom fabricated on-site.  A classic example is gel combs – those little plastic things we all use to form wells in our SDS-PAGE gels. For the privilege of owning one of these small pieces of plastic, a reputable manufacturer of such mini-gel apparatus will charge $37 for a pack of 5. Add in shipping costs and you’re looking at $10 a pop, for something that costs maybe 10c to make.

So, SketchUp, Repetier, and PrintrBot to the rescue…


That’s a custom 7-well 1.5mm comb. The reason we did this is to load more sample.  A regular 10-well comb has 10mm deep wells, 5mm wide, so they hold ~75μl each. These wells are 12mm deep and 7mm wide, so they hold 126μl each (previously we had to use tape to join together 2 wells of a 15 well comb to make a wide lane).

This one was printed at 0.15mm layer height using MakerBot PLA filament at 225C with solid rectilinear infill. It took about 10 minutes to design and 16 minutes to print, and uses about 900mm of filament, so assuming a cost of 13c per meter** that’s a 12c material cost. If it breaks or wears out, who cares?  We could print a brand new one every month for 6 years still be ahead on cost. And we can customize the size for whatever sample is needed.

The STL file for this, plus those for standard 10 well and 15 well combs (for the mini-gel box maker known as “big green”), are in this zip folder. I also threw in the Sketchup file with a blank comb-body so you can draw in the lines and use the push/pull tool to design custom well sizes, as we did here for the 7 well version.



**PLA density = 1.24kg per liter
A 1kg roll costs ~$45 depending on where you source it
Diameter=1.75mm, radius 0.875mm, pi R squared and all that malarky, so 1 meter = 2.405 cm3
This 2.405cm3 weighs 2.982 grams.
So a 1kg spool has 335 meters, i.e. 13.4c per meter

Fun with 3D printing

One of the latest things we have in the lab’ is a 3D printer – a PrintrBot Simple Metal. I bought it over the summer and assembled it from a kit, which took about 5 hours. There are lots of things available to download and print from Thingiverse, or the NIH 3D print exchange, but if you want to make things from scratch, you need to learn to design in 3D using a program such as Sketchup. It’s free to download but there’s a steep learning curve and this was a big obstacle for me.  Now I’m over that initial hump however, we can make things for the lab…

3D printed door-handle extension

The lab’ door opens outward, so opening it from the inside is easy when you’re laden with stuff or just wearing gloves – simply push and your elbow.  BUT, if you’re outside and want to get in, you can’t pull the door handle with your elbow.  So, I designed an extension to bolt onto the handle, providing a hook so you can pull the door open with your forearm, without touching anything with your hands.  Here’s the finished article…Doorpull1

The .STL file is available here (in a zip folder because web host will not allow direct hosting of STL files) if you want to print your own. The screws used were standard 3/4″ steel sheet metal screws, the kind used for air duct work and available in packs of 100 at Home Depot.  There’s a tab on the lower piece which grips against the ell in the metal handle, preventing it from spinning around. This one is for right handed opening doors, but in the next few days we plan to make one for left-handed doors too, and will update the STL then. The STL also contains some support material that has to be cut away after printing.

Trough for multi-pipeting small amounts

We use a Seahorse XF96 in the lab’. Each well has 4 drug-loading ports, but they only hold about 25 ul each. If you’re loading small amounts of expensive mitochondrial inhibitors (rotenone, FCCP etc.) the troughs typically available from lab-ware suppliers are just too big – twice as long as necessary and way too deep…


Our 3D printed version is a lot smaller, holding about 2ml instead of the usual 20-30 ml. Below is a picture, and the STL file is available here.


We’ve also played around with a few small dishes and chambers for patch clamping, various tube racks and holders, and some accessories for the PrintrBot itself. One issue we’ve come across is the water-tightness of flat printed surfaces – even with solid infill we seem to always end up with some leaks (hence the trough above was designed with angled walls that provide a much tighter seal).  Also we’re not sure yet about the long-term durability of PLA in a lab setting.  It’s a biodegradable corn plastic (polylactic acid), so might not hold up well to autoclaving etc. (we already had a tube rack deform when someone accidentally left the water bath cranked up to 70C).

We’ll be posting more STL models as they come.