September 30, 2013
A few years ago, in my programming day-job, we had a customer who we were providing with software components and a bit of custom development. While this was going on, we had a sequence of meetings with them in which we pitched several possible system designs, explaining how we could help them use our components in various ways.
After this had been going on for a while, our contact at the customer had to take us to one side. He was gentle with us: “Look, you seem to have the idea that we’re looking for some kind of ongoing consultancy from you”, he said. “We’re really not. We like your tools, and we’re happy to pay for them, but that’s all we need from you. We’ll take it from there”.
And that’s what I think about whenever I read anything like this:
Elsevier is receiving an increasing number of content mining requests and we are developing solutions to meet customer needs. […] We wish to understand our customers’ text mining requirements and as practically every content mining request has a different goal and there is not a common solution to provide this. Consequently we request that customers looking to mine our content should speak to their Elsevier Account Manager.
Even if we assume generously that this is a genuine attempt to be helpful and not just a land-grab, it’s WRONG WRONG WRONG WRONG WRONG.
No, Elsevier. Your customers’ text mining requirements are very, very simple. Every content mining request has exactly the same goal and there is a common solution to provide this. That solution is: get out of the way.
No-one needs Elsevier’s (or Wiley’s or Springer’s) help with text-mining. No-one wants them as partners. No-one needs their APIs. All anyone wants is to get hold of the papers. That’s all. The only role of the publisher in this process is not to impede it.
Publishers: your job is to publish (“make public”), then step aside and let the world make use of what you’ve published.
September 28, 2013
Anyone who’s found the SV-POW! Tutorials useful will also like the excellent, detailed osteology posts on Tom Carr’s newish blog Tyrannosauroidea Central. Highly recommended — especially for those, like me, who have a lot to learn about skulls.
Here are the osteology posts so far:
September 26, 2013
I started teaching fifteen years ago, as a graduate student at the University of Oklahoma in the spring of 1998. This document is a summary of everything I’ve learned about how students learn from then up until now. I’m setting it down in print because I found myself giving the same advice over and over again to students in one-on-one sessions—and at least for some of them, it’s made a difference.
Here’s the summary. The rationale for each point is explained in more detail below.
- Learn how you learn.
- Use your solo study time to build things.
- Use your group study time to explain things to other people, and to have them explain things to you.
- Focus on the stuff that scares you; use your fear as an ignorance-detector.
- Review everything on a regular basis—for a given exam, daily if possible.
- Spread out your study time so you don’t study past the point of diminishing returns.
- Spend as much time in lab as possible.
- Learn to ask for help.
1. Learn how you learn.
All of the rest of this advice will be many times more effective once you learn how you learn. Some people are visual learners, some verbal, some more narrative, some more spatial. I myself am visual all the way. I can really struggle with written descriptions, but if I draw something a couple of times, it will be in my head forever. I have a colleague who is just the opposite, and her preferred study method is to organize everything into giant tables. Now, I don’t know a ton about all the different learning modes, but other people do, and most schools have some kind of education, counseling, or student services office with people who can help you figure this out. If you don’t have access to resources like that, fear not: you can probably diagnose your strongest learning mode on your own, by straightforward experimentation. Observe your information consumption—what kinds of things do you gravitate toward, and what kinds of explanations do you struggle with?
2. Build things.
When you study, don’t just read your notes or watch videos. Build things. My very first question when students come to me about studying is, “What are you building when you study?” I don’t care if it is sketches or tables or flashcards or posters or interpretive dance—that’s for you to figure out (see point ). But whatever your preferred avenue of expression, if you spend at least part of your study time making things, you will engage your motor neurons, which is a way of coercing your interneurons into actually thinking about the output. And that will help fix the information in your brain. In short, active learning beats passive learning. And as a bonus, you’ll have your own customized notes that you can return to later (for example, when you’re studying for boards).
3. Study with a group, and explain things to each other.
In all of my time teaching anatomy at four different universities, it has always been true that the students who did the best were part of effective study groups. It’s not just autocorrelation, because struggling students improve when they join effective study groups. I think that this is because people in effective study groups spend their time asking each other questions, not just to quiz each other, but primarily in the vein of, “I don’t understand this, can you please explain it to me.” (Hint: if you don’t do that in your study group, maybe your group is not effective. The fix is obvious.) And when you try to explain something to someone else, you will rapidly find out what you actually understand versus what you only thought you understood. And when other people explain things to you, at best you are getting tutored, and at worst they are finding their own weaknesses, although ideally both things go on at once, and both parties benefit.
I reckon that about half of what I learned in graduate school, I learned from my fellow grad students. I am pretty sure that my advisors understood and anticipated that, and deliberately fostered environments in which peer-to-peer teaching could flourish. In small group work you can get more focused, individual attention than you can in a lecture hall with dozens or hundreds of other people. Don’t only study in groups—some solo study is necessary to firm things up for yourself, and to build your own tools (see point )—but don’t only study on your own, either.
4. Study what you’re afraid of.
Use fear and anxiety to your advantage: let them direct you to study what you’re afraid of. Think of your study time as a bug hunt, in which you systematically identify your weaknesses and deal with them. If you know the lungs cold but the thought of cardiac autonomics causes your pulse to spike, then you already know where you need to put the time in. Use confusion and fear as diagnostics for areas you need to work on.
5. Review everything regularly.
Repetition beats cramming, for at least a couple of reasons. One is that anatomy, like most subjects dealing with nature, is a continuum. But you tend to get it delivered in 50-minute chunks, with the inherent continuity broken up into more-or-less arbitrary bins (“hip”, “thigh”, “knee”, etc.). One of your primary jobs, then, is to take this string of chunks and mentally turn it back into a continuum: to find the joins between adjacent lectures, and the overarching principles that unite them all. The best way I know to do this is to review everything on a regular basis—daily, if possible. If you have two hours blocked out to study, spend the first 30 minutes going over your notes* from all of the previous lectures, then get on to the day’s topic. Next time, whatever you studied today will be another link in the chain. In time, you will see how today’s material links back to previous lectures, and forward to later ones.
* The whole point of notes (by which I mean sketches, flashcards, etc.—whatever it is that you are building during your study time) is to serve as a funnel between the course material and your brain. So useful notes have to package things so they are easier to understand. If the map is as complicated as the territory, it’s not really a map. It’s okay if your first set of notes is overly long and ugly, because your first set of notes should not be your only set. As your understanding improves, build new tools (i.e., make new notes) that reflect that.
6. Don’t study past the point of diminishing returns.
This is the other reason why repetition beats cramming. You need to revisit the material multiple times because the amount you can learn in one session is finite. There is a real biological basis for this: the neurotransmitters and receptors involved in shifting information from short-term memory to long-term memory need a certain amount of time to recharge, and that time is measured in hours, not minutes. Somewhere around the three hour mark, your brain will have absorbed as much as it can for that session. You can keep putting more stuff into short-term memory, but it won’t get copied to long-term memory. Get up and do something else, and come back to it that evening, or the next day. (“Do something else” can mean “do useful work for your other classes”, especially if the work for other classes is different in kind, like practicing techniques.) The more times you revisit the material, the more opportunities you have to successfully copy it into long-term memory, the more you actually learn.
This may sound crazy, because we have all had episodes of sustained effort lasting more than three hours, like a day at work. The difference is that at work, you’re not trying to remember everything, and when you study, that is precisely what you are trying to do. I have had students tell me that they are studying for six to eight hours at a time and they’re still not getting it. This is heartbreaking—such long uninterrupted sessions guarantee that at least half of that time is simply wasted. You absolutely can study effectively for six or eight hours a day, you just need to break up the time: two hours in the morning, three in the afternoon, another three in the evening, so your neurotransmitters can recharge in between. You will hear people say things like, “Study smarter, not harder.” Mostly this boils down to, “Study actively and more frequently, not passively or for too long at a stretch.”
7. Spend as much time as you can in the lab.
Spend as much time as you can in lab, not just on dissecting days, but anytime the lab is open. We have a saying, that you learn concepts in the lecture hall but you learn anatomy in the lab. The time with the cadavers is a gift, the only opportunity you will have for the rest of your career to spend dozens of hours getting tactile experience cutting on patients who don’t bleed and can’t code. Use it. “But what about my friends, family, pets, hobbies—my life?” Your life extends ahead of you for decades. Your time in the anatomy lab lasts for a few weeks at most.
8. Learn to ask for help.
The last thing I have to say is the most important: learn to ask for help. I am on one of the student performance committees at WesternU, where students end up when they fail courses. There are a constellation of things that may cause a student to fail a course, but one of the big ones is trying to bull through alone. I get it—you were hot stuff in high school, maybe college too, the big fish in the small pond, and you’re used to being the smartest person in the room. Well, now you’re in med school, and your previous specialness is now the default for everyone here. It is very likely that college did not prepare you to work anywhere near as hard as you will have to now. The good news is that you are therefore untested, so even you don’t know how much you are capable of. In the next few years, you will find reserves of strength that you did not know you possess—but you will not do it alone. Asking for help is not a sign of weakness. It means that you are strong enough to be honest about your limitations, which is the first step to overcoming them. In my experience, more people fail out of pride than from lack of ability.
Whom should you ask for help? It depends on your situation, but a short list includes peers, TAs, professors, student services, counselors, and the school administration. If you don’t know whom to ask, just ask someone, and they’ll probably point you in the right direction. Usually knowing whom to ask is not the hurdle—it’s being willing to ask in the first place. If you are struggling in a course and you haven’t been to talk to the instructor, then you’re not trying as hard as you could be. You have committed years of your life to this. Isn’t succeeding more important than polishing your pride while the ship sinks? Learn to ask for help.
September 25, 2013
This beauty is by Bryan Riolo, aka Algoroth on DeviantART, who also let me use his giant space Cthulhu for my Collect Call of Cthulhu over on Echo Station 5-7. Update: and here, belatedly, is a link to the piece on DA, with Bryan’s thoughts on it.
I love the sense of scale here, with paralititans striding through the surf, the chiaroscuro, and the sheer amount of stuff going on. It reminds me of William Stout’s murals, and lots of atmospheric classic paintings. Sure, there’s a theropod getting his guts rearranged, which I’m always up for, but that’s literally just a sidelight (or sidedark?) in this epic image. In short, I’m diggin’ the art in this paleoart.
For more sauropods stomping theropods, see:
- Genesis of an instant paleo-art classic
- Sauropods stomping theropods: a much neglected theme in palaeo-art
- Sauropods stomping theropods redux
- Brian Engh: Stomp time!
And if your definition of ‘stomping’ encompasses pooping on, vomiting at, and blowing away with sheer awesomeness, you may also enjoy:
September 24, 2013
I woke up this morning to find its third substantial review waiting for me.
That means that this paper has now accumulated as much useful feedback in the twenty-seven hours since I submitted it as any previous submission I’ve ever made.
It’s worth reviewing the timeline here:
- Monday 23rd September, 1:19 am: I completed the submission process.
- 7:03 am: the preprint was published. It took less than six hours.
- 10:52 am: received a careful, detailed review from Emanuel Tschopp. It took less than four hours from publication, and so of course less than ten from submission.
- About 5:00 pm: received a second review, this one from Mark Robinson. (I don’t know the exact time because PeerJ’s page doesn’t show an actual timestamp, just “21 hours ago”.)
- Tuesday 24th September, about 4:00 am: received a third review, this from ceratopsian-jockey and open-science guru Andy Farke.
Total time from submission to receiving three substantial reviews: about 27 hours.
It’s worth contrasting that with the times taken to get from submission to the receipt of reviews — usually only two of them — when going through the traditional journal route. Here are a few of mine:
- Diplodocoid phylogenetic nomenclature at the Journal of Paleontology, 2004-5 (the first reviews I ever received): three months and 14 days.
- Revised version of the same paper at PaleoBios, 2005 (my first published paper): one month and 10 days.
- Xenoposeidon description at Palaeontology, 2006: three months and 19 days, although that included a delay as the handling editor sent it to a third, tie-breaking, reviewer.
- Brachiosaurus revision at the Journal of Vertebrate Paleontology, 2008: one month and 11 days.
- Sauropod neck anatomy (eventually to be published in a very different form in PeerJ) at Paleobiology: five months and two days.
- Trivial correction to the Brachiosaurus revision at the Journal of Vertebrate Paleontology, 2010: five months and 11 days, bizarrely for a half-page paper.
Despite the wide variations in submission-to-review time at these journals, it’s clear that you can expect to wait at least a month before getting any feedback at all on your submission at traditional journals. Even PeerJ took 19 days to get the reviews of our neck-anatomy paper back to us.
So I am now pretty such sold on the pre-printing route. As well as getting this early version of the paper out there early so that other palaeontologists can benefit from it (and so that we can’t be pre-emptively plagiarised), issuing a preprint has meant that we’ve got really useful feedback very quickly.
I highly recommend this route.
By the way, in case anyone’s wondering, PeerJ Preprints is not only for manuscripts that are destined for PeerJ proper. They’re perfectly happy for you to use their service as a place to gather feedback for your work before submitting it elsewhere. So even if your work is destined for, say, JVP, there’s a lot to be gained by preprinting it first.
September 23, 2013
I was very pleased, on checking my email this morning, to see that my and Matt’s new paper, The neck of Barosaurus was not only longer but also wider than those of Diplodocus and other diplodocines, is now up as a PeerJ preprint!
I was pleased partly because of the very quick work on PeerJ’s part. I submitted the preprint at 1:22am last night, then went to bed. Almost immediately I got an automatic email from PeerJ saying:
Thank you for submitting your manuscript, “The neck of Barosaurus was not only longer but also wider than those of Diplodocus and other diplodocines” (#2013:09:838:0:0:CHECK:P) – it has now been received by PeerJ PrePrints.
Next, it will be checked by PeerJ staff, who will notify you if any alterations are required to the manuscript or accompanying files.
If the PrePrint successfully passes these checks, it will be made public.
You will receive notification by email at each stage of this process; you can also check the status of your manuscript at any time.
Lots to like here: the quickness of the response, the promise of automatic email updates, and the one-click link to check on progress (as opposed to the usual maze of Manuscript Central options to navigate).
Sure enough, a couple of hours later the next automatic email arrived, telling me that Matt had accepted PeerJ’s email invitation to be recognised as the co-author of the submission.
And one hour ago, just as I was crawling out of bed, I got the notification that the preprint is up. That simple.
I’m also pleased because we managed to get this baby written so quickly. It started life as our talk at SVPCA in Edinburgh (Taylor and Wedel 2013a), which we delivered 25 days ago having put it together mostly in a few days running up to the conference — so it’s zero to sixty in less than a month. Every year we promise ourselves that we’ll write up our talks, and we never seem to get around to it, but this year I started writing on the train back from Edinburgh. By the time I got home I had enough of a hunk of text to keep me working on it, and so we were able to push through in what, for us, is record time.
Now here’s what we’d like:
We want this paper’s time as a preprint to be time well spent — which means that we want to improve it. To do that, we need your reviews. Assuming we get some useful comments, we plan to release an updated version pretty soon; and after some number of iterations, we’ll submit the resulting paper as a full-fledged PeerJ paper.
So if you know anything about sauropods, about vertebra, about deformation, about ecology, or even about grammar or punctuation, please do us a favour: read the preprint, then get over to its PeerJ page and leave your feedback. You’ll be helping us to improve the scientific record. We’ll acknowledge substantial comments in the final paper, but even the pickiest comments are appreciated.
Because we want to encourage this approach to bringing papers to publication, we’d ask you please do not post comments about the paper here on SV-POW!. Please post them on the PeerJ preprint page. We’ve leaving comments here open for discussion of the preprinting processes, but not the scientific content.
- Taylor, Michael P., and Mathew J. Wedel. 2013a. Barosaurus revisited: the concept of Barosaurus (Dinosauria: Sauropoda) is based on erroneously referred specimens. (Talk given as: Barosaurus revisited: the concept of Barosaurus (Dinosauria: Sauropoda) is not based on erroneously referred specimens.) pp. 37-38 in Stig Walsh, Nick Fraser, Stephen Brusatte, Jeff Liston and Vicen Carrió (eds.), Programme and Abstracts, 61st Symposium on Vertebrae Palaeontology and Comparative Anatomy, Edinburgh, UK, 27th-30th August 2013. 33 pp.
- Taylor, Michael P., and Mathew J. Wedel. 2013b. The neck of Barosaurus was not only longer but also wider than those of Diplodocus and other diplodocines. PeerJ PrePrints 1:e67v1 http://dx.doi.org/10.7287/peerj.preprints.67v1
September 20, 2013
I was astonished yesterday to read Understanding and addressing research misconduct, written by Linda Lavelle, Elsevier’s General Counsel, and apparently a specialist in publication ethics:
While uncredited text constitutes copyright infringement (plagiarism) in most cases, it is not copyright infringement to use the ideas of another. The amount of text that constitutes plagiarism versus ‘fair use’ is also uncertain — under the copyright law, this is a multi-prong test.
So here (right in the first paragraph of Lavelle’s article) we see copyright infringement equated with plagiarism. And then, for good measure, the confusion is hammered home by the depiction of fair use (a defence against accusations of copyright violation) depicted as a defence against accusations of plagiarism.
This is flatly wrong. Plagiarism and copyright violation are not the same thing. Not even close.
First, plagiarism is a violation of academic norms but not illegal; copyright violation is illegal, but in truth pretty ubiquitous in academia. (Where did you get that PDF?)
Second, plagiarism is an offence against the author, while copyright violation is an offence against the copyright holder. In traditional academic publishing, they are usually not the same person, due to the ubiquity of copyright transfer agreements (CTAs).
Third, plagiarism applies when ideas are copied, whereas copyright violation occurs only when a specific fixed expression (e.g. sequence of words) is copied.
Fourth, avoiding plagiarism is about properly apportioning intellectual credit, whereas copyright is about maintaining revenue streams.
Let’s consider four cases (with good outcomes is green and bad ones in red):
- I copy big chunks of Jeff Wilson’s (2002) sauropod phylogeny paper (which is copyright the Linnean Society of London) and paste it into my own new paper without attribution. This is both plagiarism against Wilson and copyright violation against the Linnean Society.
- I copy big chunks of Wilson’s paper and paste it into mine, attributing it to him. This is not plagiarism, but copyright violation against the Linnean Society.
- I copy big chunks of Rigg’s (1904) Brachiosaurus monograph (which is out of copyright and in the public domain) into my own new paper without attribution. This is plagiarism against Riggs, but not copyright violation.
- I copy big chunks of Rigg’s paper and paste it into mine with attribution. This is neither plagiarism nor copyright violation.
Plagiarism is about the failure to properly attribute the authorship of copied material (whether copies of ideas or of text or images). Copyright violation is about failure to pay for the use of the material.
Which of the two issues you care more about will depend on whether you’re in a situation where intellectual credit or money is more important — in other words, whether you’re an author or a copyright holder. For this reason, researchers tend to care deeply when someone plagiarises their work but to be perfectly happy for people to violate copyright by distributing copies of their papers. Whereas publishers, who have no authorship contribution to defend, care deeply about copyright violation.
One of the great things about the Creative Commons Attribution Licence (CC By) is that it effectively makes plagiarism illegal. It requires that attribution be maintained as a condition of the licence; so if attribution is absent, the licence does not pertain; which means the plagiariser’s use of the work is not covered by it. And that means it’s copyright violation. It’s a neat bit of legal ju-jitsu.
- Riggs, Elmer S. 1904. Structure and relationships of opisthocoelian dinosaurs. Part II, the Brachiosauridae. Field Columbian Museum, Geological Series 2:229-247, plus plates LXXI-LXXV.
- Wilson, Jeffrey A. 2002. Sauropod dinosaur phylogeny: critique and cladistic analysis. Zoological Journal of the Linnean Society 136:217-276.