February 29, 2016
Functional Anatomy of the Vertebrates: An Evolutionary Perspective, by Liem et al. (2001), is by some distance my favorite comparative vertebrate anatomy text. When I was a n00b at Berkeley, Marvalee Wake assigned it to me as preparatory reading for my qualifying exams.
The best textbooks, like Knut Schmidt-Nielsen’s Animal Physiology (which deserves a post or even series of its own sometime), have a clarity of writing and illustration that makes the fundamentals of life seem not only comprehensible, but almost inevitable – without losing sight of the fact that nature is complex and we don’t know everything yet. FAotV has both qualities, in spades.
I’m writing about this now because Willy Bemis, second author on FAotV, has just made ALL of the book’s illustrations available for free on his website, in a series of 22 PowerPoint files that correspond to the 22 chapters of the book. All told they add up to about 155 Mb, which is trivial – even the $5 jump drives in the checkout lanes at department stores have five to ten times as much space.
Of course, to get the full benefit you should also pick up a copy of the book. I see used copies going for under $40 in a lot of places online. Mine will have pride of place on my bookshelf until I enter the taphonomic lottery. And I’ll be raiding these PPTs for images from now until then, too.
So do the right thing, and go download this stuff, and use it. Be sure to credit Liem et al. (2001) for the images, and thank Willy Bemis for making them all available. It’s a huge gift to the field. Here’s that link again.
But wait – that’s not all! Starting on June 28, Dr. Bemis will be one of six faculty members from Cornell and the University of Queensland teaching a 4-week massively open online course (MOOC) on sharks. Freakin’ sharks, man!
“What did you do this summer? Hang out and play Nintendo?”
“Yep. Oh, and I also took a course on freakin’ sharks from some awesome shark experts. You?”
As the “massively open” part implies, the course is free, although you have the option of spending $49 to get a certificate of completion (assuming you finish satisfactorily). Go here to register or get more info.
- Liem, K.F., Bemis, W.E., Walker, W.F., and Grande, L. 2001. Functional Anatomy of the Vertebrates. (3rd ed.). Thomson/Brooks Cole, Belmont, CA.
As we all know, University libraries have to pay expensive subscription fees to scholarly publishers such as Elsevier, Springer, Wiley and Informa, so that their researchers can read articles written by their colleagues and donated to those publishers. Controversially (and maybe illegally), when negotiating contracts with libraries, publishers often insist on confidentiality clauses — so that librarians are not allowed to disclose how much they are paying. The result is an opaque market with no downward pressure on prices, hence the current outrageously high prices, which are rising much more quickly than inflation even as publishers’ costs shrink due to the transition to electronic publishing.
On Thursday 11 April 2013, Oxford University hosted a conference called Rigour and Openness in 21st Century Science. The evening event was a debate on the subject Evolution or Revolution In Science Communication. During this debate, Stephen Curry of Imperial College noted that his librarian isn’t allowed to tell him how much they pay for Elsevier journals. This is the response of David Tempest, Elsevier’s Deputy Director of Universal Sustainable Research Access.
Heres’ a transcript
Curry [in reference to the previous answer]: I’m glad David Tempest is so interested in librarians being able to make costs transparent to their users, because at my university, Imperial College, my chief librarian can not tell me how much she pays for Elsevier journals because she’s bound by a confidentiality clause. Would you like to address that?
[Loud applause for the question]
Tempest: Well, indeed there are confidentiality clauses inherent in the system, in our Freedom Collections. The Freedom Collections do give a lot of choice and there is a lot of discount in there to the librarians. And the use, and the cost per use has been dropping dramatically, year on year. And so we have to ensure that, in order to have fair competition between different countries, that we have this level of confidentiality to make that work. Otherwise everybody would drive down, drive down, drive drive drive, and that would mean that …
[The last part is drowned in the laughter of the audience.]
So there you have it: confidentiality clauses exist because otherwise everybody would drive down prices. And we can’t have that, can we?
(Is this extracted segment of video unfairly misrepresenting Tempest? No. To see that for yourself, I highly recommend that you watch the video of the whole debate. It’s long — nearly two hours — but well worth the time. The section I used here starts at 1:09:50.)
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 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.
July 9, 2013
Robin Osborne, professor of ancient history at King’s College, Cambridge, had an article in the Guardian yesterday entitled “Why open access makes no sense“. It was described by Peter Coles as “a spectacularly insular and arrogant argument”, by Peter Webster as an “Amazingly wrong-headed piece” and by Glyn Moody as “easily the most arrogant & dim-witted article I’ve ever read on OA”.
Here’s my response (posted as a comment on the original article):
At a time when the world as a whole is waking up to the open-access imperative, it breaks my heart to read this fusty, elitist, reactionary piece, in which Professor Osborne ends up arguing strongly for his own irrelevance. What a tragic lack of vision, and of ambition.
There is still a discussion to be had over what routes to take to universal open access, how quickly to move, and what other collateral changes need to be made (such as changing how research is evaluated for the purposes of job-searches and promotion). But Osborne’s entitled bleat is no part of that discussion. He has opted out.
The fundamental argument for providing open access to academic research is that research that is funded by the tax-payer should be available to the tax-payer.
That is not the fundamental argument for providing open access (although it’s certainly a compelling secondary one). The fundamental argument is that the job of a researcher is to create new knowledge and understanding; and that it’s insane to then take that new knowledge and understanding and lock it up where only a tiny proportion of the population can benefit from it. That’s true whether the research is funded publicly or by a private charity.
The problem is that the two situations are quite different. In the first case [academic research], I propose both the research questions and the dataset to which I apply them. In the second [commercial research] the company commissioning the work supplies the questions.
Osborne’s position here seem to be that because he is more privileged than a commercial researcher in one respect (being allowed to choose the subject of his research) he should also be more privileged in another (being allowed to choose to restrict his results to an elite). How can such an attitude be explained? I find it quite baffling. Why would allowing researchers to choose their own subjects mean that funders would be happy to allow the results to be hidden from the world?
Publishing research is a pedagogical exercise, a way of teaching others
Yes. Which is precisely why there is no justification for withholding it from those others.
At the end of the day the paper published in a Gold open access journal becomes less widely read. […] UK scholars who are obliged to publish in Gold open access journals will end up publishing in journals that are less international and, for all that access to them is cost-free, are less accessed in fact. UK research published through Gold open access will end up being ignored.
As a simple matter of statistics, this is flatly incorrect. Open-access papers are read, and cited, significantly more than paywalled papers. The meta-analysis of Swan (2010) surveyed 31 previous studies of the open-access citation advantage, showing that 27 of them found advantages of between 45% are 600%. I did a rough-and-ready calculation on the final table of that report, averaging the citation advantages given for each of ten academic fields (using the midpoints of ranges when given), and found that on average open-access articles are cited 176% more often — that is, 2.76 times as often — as non-open.
There can be no such thing as free access to academic research. Academic research is not something to which free access is possible.
… because saying it twice makes it more true.
Like it or not, the primary beneficiary of research funding is the researcher, who has managed to deepen their understanding by working on a particular dataset.
Just supposing this strange assertion is true (which I don’t at all accept), I’m left wondering what Osborne thinks the actual purpose of his research is. On what basis does he think our taxes should pay him to investigate questions which (as he himself reminds us) he has chosen as being of interest to him? Does he honestly believe that the state owes him not just a living, but a living doing the work that he chooses on the subject that he chooses with no benefit accruing to anyone but him?
No, it won’t do. We fund research so that we can all be enriched by the new knowledge, not just an entited elite. Open access is not just an economic necessity, it’s a moral imperative.
October 27, 2011
In a comment on an previous post, wycx articulated a position that sounds all too familiar:
Until the impact factors and prestige/credibility of open access journals are as high as their closed equivalents AND university administrators and funding agencies stop quantifying academic performance via impact factors, I do not see much changing.
I have heard a lot of people say things like this in the last couple of months. It makes pretty depressing reading.
But how true is it? And can we do anything to change it?
Well, first up that big AND in wycx’s comment should be an OR. When the prestige/credibility of open access journals is as high as their closed counterparts OR university administrators and funding agencies stop quantifying academic performance via impact factors, the push to publish in non-open venues will go away. Either open access journals will start winning the assessment game; or, better still, we can all stop stop playing that stupid game and just place our papers where they’ll be read by the relevant people.
But there’s a more fundamental issue here. That kind of comment sees researchers as passive victims. The story it tells (whether or not this was wycx’s intention) is that there’s nothing we can do to change the situation.
But that’s not true. There are actually quite a few things we can do.
Preferentially submit to open-access journals
This is the big one, of course. It’s been pointed out many times in the comments to these posts, rightly, that not everyone has the luxury of academic freedom that comes from being a professional programmer, and I do accept that career academics may have circumstances that make non-open venues very attractive — especially when they have something that might get into Science or Nature.
But just because someone is not in a position to implement a blanket ban on submitting to non-open venues, that’s no reason not to favour open-access venues — even to favour them very strongly. I have the sense that openness is at least a factor for more and more people; I would love to see it become a more significant factor for more researchers.
I strongly suspect that nothing else we do is more important than favouring open-access venues for our own papers. The attractiveness of certain non-open venues comes from the quality of the work that is published in them, and because of that attractiveness, people send more good work into those silos. But once that circle begins to break, things will move quickly. There’s that open-access journals can’t be as highly cited (and so as prestigious) as S&N — in fact, one of the big landmark days that I am looking forward to is when an open journal has the highest Impact Factor in science.
Do not review for non-open journals
I’ve written about this a lot, so I won’t rehash the arguments in detail. In short: your unpaid volunteer work should be in the service of the whole world, not the dividends of commercial publishers’ shareholders.
Do not edit for non-open journals
This follows on not reviewing for non-open journals. Again, I understand why some researchers need to do this: I have a friend who edits for an Elsevier journal, frankly because he or she needs the money. But these can be, and should be, the exception.
And we’re starting to see this happening. My friend is keen to stop working for Elsevier as soon as it’s financially possible. Steve Wheeler recently resigned as co-editor of Interactive Learning Environments, a Taylor and Francis journal. Peter Suber once compiled a list of entire editorial boards that have resigned en masse to start open-access journals.
As with reviewing, the point is of course not just to withdraw effort from non-open publishers; it’s to redirect that effort to open publishers, so that the whole world benefits from it.
Influence conferences to make proceedings open access
It was great that the the Geological Society hosted the excellent conference Dinosaurs and Other Extinct Saurians: A Historical Perspective (written up at Tetrapod Zoology [part 1], [part 2]). But as we’ve noted before, the proceedings volume is non-open and absurdly expensive: $190 at amazon.com, £95 at amazon.co.uk. The result is obvious: no-one is going to buy it, and the papers will not get read. (Exception: my own contribution is freely available, but only because I played a trick with the Geol Soc’s copyright assignment mechanism.)
I have another conference coming up soon that will generate a proceedings volume. So this time, I have been in contact with the conference organisers ahead of time to express my preference for open-access proceedings. Happily, they are in agreement that this is desirable and even important, so hopefully we should see a special issue of a well-regarded journal at some point in the next few years. (Sorry to be vague, but the details are not yet settled. We’ll let you know when it happens.)
Influence funding bodies to mandate open access
This is one for academics much more senior and influential than I am. But we know that several of the big funding bodies, including the Wellcome Trust (UK) and the National Institutes of Health (USA), are mandating as a condition of awarding grants that the research outputs must be freely available. This is a big win: those of us with enough influence can encourage other funding bodies to adopt similar policies.
Influence universities to mandate open access
An increasing number of universities also have, or are adopting, open-access mandates for their research outputs, including MIT (USA) and UCL (UK). I wonder what influence each of us has on the policies of our own universities? Some of us much more than others, of course. I will at least be asking questions around the University of Bristol, to see whether moves can be made in that direction.
Spread the word!
… and finally, there is one thing that we can all do to help, and that is simply to spread the word. Blog about open-access papers, tell your friends which are the good publishers, talk about the importance of open access in the pub. Let the world know that the status quo can be and must be shifted!
Perhaps even more important, as I hope I have shown, it is shifting. Universities like MIT and UCL are not minor-league (in fact the most recent Times Higher Education rankings list them at number 7 and number 17 in the world). Contra the negative tone of the comment that I quoted at the start of this article, open access is becoming an increasingly important issue not just among a few malcontents such as myself but with the most influential and important researchers and institutions.
We live in exciting times.
Finally: it may seem strange, but I only found out today that this is Open Access week (Ocotober 24-30), so it’s appropriate that I’ve found myself writing so much about it.
In celebration of, or at least in resonance with, Open Access Week, the Royal Society has just announced that it is permanently open-accessing all of its articles that are 70 years old and more. That makes a very important historical resource available to the world. Good times.
October 4, 2011
On the right, under the list of Pages, is a new one called Human anatomy study materials. It’s a bunch of stuff I’ve made for students over the years. As I wrote on the page, if you like them, use them; if not, ignore ‘em; and if you find errors, please let me know.