Moral dimensions of Open, part 0: why this matters
March 31, 2016
From 19th-22nd April this year, it will be my privilege to participate in OSI2016, the first annual meeting of the Open Scholarship Initiative. (I do think this project could have come up with a name that has a different acronym: OSI was previously the Open Society Institute, which was instrumental in getting open access off the ground — not to mention the Open System Interconnection seven-layer networking model. But never mind.)
The OSI meeting is not a conventional conference. Instead, much of its work will consist of meetings of fifteen separate groups, each considering and discussing a different question or issue: for example, What Is Publishing? What Is Open? Who Decides? Peer Review. Embargoes. I will be working in the Moral Dimensions Of Open group, along with a stellar (and slightly intimidating) cast.
I’m delighted to be on this group, because my view is that it’s the most foundational of them all. Everything else we do in the Open space flows from our moral position on Open. If we get this right, then even the thorniest matters of implementation become much clearer — because we have a foundation to build on.
Now, I know this attitude is not universally held. Publishing consultant Joe Esposito gave a very different perspective in an interview with Richard Poynder in 2013 (and let me emphasise how much I appreciate Joe’s candour in this — I am sure his views are shared by plenty of other people who are less forthcoming, and it’s very helpful to have them laid out clearly):
Q: What in your view is the single most important task that the OA movement should focus on today?
A: Getting rid of the idealists. Let pragmatism abound!
Joe is proudly pragmatic about ways of making money from publishing,
whether via paywalls or APCs, and elsewhere has argued that:
Access is a privilege of membership (e.g., being a student at a university), not a right. Can we stop this debate now and simply agree that we have no common ground upon which to base a conversation?
So perhaps the most fundamental disagreements on open scholarship are not between those with different views about its moral basis, but between those who have a view and those who avowedly have none. If open access, for example, is just a different economic model for publishers, then we may find that some of our fellow-travellers never had the same intentions as us, but merely happened to be travelling on the same road for a while.
So in remaking scholarship, and especially scholarly publishing, we need to bear in mind the parable told by G. K. Chesterton in the introduction to his book Heretics:
Suppose that a great commotion arises in the street about something, let us say a lamp-post, which many influential persons desire to pull down. A grey-clad monk, who is the spirit of the Middle Ages, is approached upon the matter, and begins to say, in the arid manner of the Schoolmen, “Let us first of all consider, my brethren, the value of Light. If Light be in itself good—” At this point he is somewhat excusably knocked down. All the people make a rush for the lamp-post, the lamp-post is down in ten minutes, and they go about congratulating each other on their unmediaeval practicality. But as things go on they do not work out so easily. Some people have pulled the lamp-post down because they wanted the electric light; some because they wanted old iron; some because they wanted darkness, because their deeds were evil. Some thought it not enough of a lamp-post, some too much; some acted because they wanted to smash municipal machinery; some because they wanted to smash something. And there is war in the night, no man knowing whom he strikes. So, gradually and inevitably, to-day, to-morrow, or the next day, there comes back the conviction that the monk was right after all, and that all depends on what is the philosophy of Light. Only what we might have discussed under the gas-lamp, we now must discuss in the dark.
That’s why, when I had the privilege of addressing the 11th Berlin conference on open access in 2013, I used my slot to remind the audience that, as my talk’s title put it, open access is about sharing, unity and sanity, not about money. Because I was addressing a more senior audience than I usually speak to — one that necessarily has to think more about practicalities, finances, ways and means — I wanted to take the opportunity to remember that those are not the issues that gave birth to open scholarship; rather, it started out as an unabashedly idealistic movement (as reading any of the three
great open-access declarations will show you). I don’t want us to walk away from that high-ground and be reduced to thinking only about practicalities, important though they are.
Publishers and their associates often say — rightly, as far as they go — that “Scientific and technical publishing is a business“. But no-one goes into that business because of the money they can make. Everyone involved in research surely chose that business because their eyes were on a higher prize. Doing and publishing research is a mission; far from “getting rid of the idealists“, we should cherish them; and we should encourage rather than curb our own idealistic tendencies.
So my first and most important conviction about the moral dimension of Open is that it exists, that it’s crucial, and that it’s absolutely not something for us to feel ashamed of, as though it’s an adolescent phase that we’ll grow out of once we become old enough and wise enough to understand pragmatism. The moral dimension is what gives us a goal for our pragmatism to work towards.
All depends on what is the philosophy of Light.
[Read on to part 1: “marginal cost is zero, so price should be zero”]
Mind you, it’s not all dead badgers in my kitchen
March 28, 2016
There’s also this:
As Orson Welles is supposed to have said: My doctor told me to stop having intimate dinners for four. Unless there are three other people.
Defleshing a badger head: a pictorial guide
March 28, 2016
There’s no sense in decapitating a badger if you’re not going to make good use of the severed head. So here’s what I did with mine. First, a reminder of the state it was in after yesterday’s adventures:
Ideally, I would have liked to skin the head — it would have made subsequent stages easier and less messy. But as I noted last time, badgers have very tough skin, and it was hard to do anything with it. I feared that the force necessary would at best damage the underlying bone, and at worst give me a nasty cut.
So I satisfied myself with trimming away the flesh collar, leaving the head-and-anterior-neck segment a little shorter, and of a suitable size to go into the saucepan:
See?
Then it was a simple matter of filling with hot water …
… then bringing it all up to a simmer, and giving it a couple of hours while I played some Skyrim and watched an episode of Elementary. Once I’d drained the water off, here’s the result of the first simmer:
As you can see (you may need to click through to make it out properly), that tough skin has contracted so hard that it’s pulled away from the skull at the top, exposing part of the distinctive midline crest.
Anyway, with the skin now softened it was relatively easy (though disgusting) to peel it off. Once all the rest of the superficial soft-tissue was gone, the massive massive muscles that attached to the midline crest were apparent.
I broke these off:
You can see one of them in the last photo. It really is a substantial piece of equipment: and you can see as well that the muscle mass going through the zygomatic arches is substantial.
You may also notice that at this stage, I’ve left the nose intact. That’s because I didn’t want to risk damaging the delicate nasal turbinates by pulling the soft-tissue away too roughly. Instead, I left it on for the second simmer:
As you can see, it came out from that with the meat much more cooked, and so easier to remove:
In my previous adventures preparing mammal skulls, I’ve found that one of the most satisfying moments is when the mandible (lower jaw) comes away from the cranium. You really feel that you’re making progress then, and it becomes much easier to reach some of the tricker areas of soft-tissue. That doesn’t happen with badgers: their jaws are permanently articulated, with cylindrical articular condyles wrapped in incomplete bone-tunnels. (I hope I can show you this properly once preparation is complete.)
Anyway, I was able to do a much better job of removing the meat this time: only scraps are left, and I was also at this point able to remove and begin cleaning the first few cervical vertebrae. I have the atlas, axis and damaged third. (I discarded the last of these, since it’s not complete.) Here’s the state of it at this point:
And that skull in right lateral view, hopefully dispelling any remaining misconceptions you may have had about badgers being cute:
As you can see, there were still plenty of scraps of hard-to-remove flesh clinging on, especially around the jaws and the base of the cranium. So it was time for simmer number three. I will spare you yet more photos of my saucepan, and instead skip straight to the skull as it appeared after this phase, and after I’d removed more of the flesh. Much nicer:
You may be wondering, what is the best way to clean the teeth of a dead and partially prepared badger skull? Sometimes the obvious answer is the right one, and this is one of those occasions. A toothbrush is the tool of choice, and it works wonders with the base of the cranium, too. (Warning: do not allow the toothbrush to re-enter civilian society after this experience.)
Here we have the skull with the mandible open:
Do not get bitten by a badger.
Skull in dorsal view:
(I will prepare nicer, scientific-quality photographs in orthogonal views once preparation is complete — as I have done for other skulls.)
One of the many things that’s impressed me about this badger is how very much meat there was on its skull. I kept it, or most of it, and now you have the privilege of seeing the skull and its soft-tissue together:
This is dramatically different from how we think of heads, or at least of how I do. I think this is because when we hear “skull”, we’ve been conditioned by years of Scooby Doo and Indiana Jones to think “human skull”. And I think that human heads much more closely match the profile of their skulls than those of badgers do theirs.
Of course this is just another way of saying that there is a lot more muscle on a badger skull, which is another way of saying that this is a seriously powerful animal. I know I keep making this point, but I think it’s a point well worth making. The world has had quite enough of this kind of thing (from here):
And its time that we all started to give badgers the credit they deserve. They are basically small bears with misleadingly endearing facial coloration.
(BTW., when I say that I kept the meat, I mean that I kept it until I’d taken that photo. Then I threw it away. I’ve not kept it permanently, I’m not a sicko. No, I’m not.)
I leave you with one of the less successful old music-hall jokes:
- First man: I say, I say I say! What’s the best way to remove the brain from a dead and partially cooked badger skull?
- Second man: Actually, there is no good way. The best I’ve found is to shove a chopstick through the foramen magnum, swirl it around to break up the tissue, then shake the bits out and repeatedly rinse.
- First man: That’s disgusting.
- Second man: I never said it wasn’t.
Here is the residue, in our sink:
Fiona, if you’re reading this: I promise I will have this all nicely cleaned up before you return from your parents’ house with the boys.
(Did I mention that Fiona had taken the boys to her parents’ house? It’s not because of the dead badger. It’s just coincidence. I think.)
Over the last couple of weeks, I’ve been fortunate enough to acquire two medium-sized native mammals, both roadkill specimens in good conditions: a fox and a badger:
But I’ve found from bitter experience that prepping out the entire skeleton of good-sized animals like these is a lot of dirty smelly work. So I decided to make things easier on myself by only prepping the skulls of these two.
Step one: remove the heads.
What follows is not pretty. Parental advisory: you should avoid this post if you feel a misguided sentimentality about the already-dead corpses of deceased animals.
I considered several approaches, as recommended by commenters on this blog and people on Twitter, but ended up taking the butcher’s approach — mostly because I have a good, sharp knife, but lack some of the tools needed for other approaches.
I took on the fox first. I cut through the skin surrounding its neck, and peeled it back far enough to reveal the neck musculature:
From there, it was pretty easy to slice away the muscles down towards the vertebrae — but impossible to get right to the vertebrae themselves, because they’re surrounded by gloop including not only muscles, but ligaments, fascia and tendons:
I’d hoped to be able to feel my way to an intervertebral joint, and ease it apart with the knife. But that turned out to be difficult. It was also going to need a lot of force, and I was worried that down in among all that gloop, I might slip and cut myself.
So I used our the axe we use for chopping firewood. It would have been terrible for dealing with the flesh, but it was fine for the bones:
Then it was the same procedure for the badger. I started by cutting a ring around the skin of the neck and peeling back.
Straight away, it was obvious that the badger is a much more serious piece of kit than the fox. It’s not as long, but it’s heavier, and much more muscular, and it has way tougher skin. I don’t know if foxes and badgers ever fight, but if they do, my money is on the badger every time. It would bite much harder and its claws are epic, too. The only thing the fox would be better at is running away.
Then, as with the fox, I sliced away the meat till I reached the bony core of the neck:
And again, the axe finished the job. I was left with a pair of decapitated corpses:
And, more importantly, a pair of heads:
Also, some evidence of my activities in the bloodstained chopping block. I hope the neighbours don’t see this and leap to the wrong conclusion:
What to do with the sadly unloved postcrania? I have no further use for them, so I decided to bury the bodies. I went down to the bottom of our garden, only to find all the sheep in the adjacent field coming over to see what I was doing:
Best stay back, sheep! Or you could be next!
I dug a hole, which is a lot more work than it looks. Predictably, given that I am England during what passes for springtime, it suddenly stared hailing while I was digging. But eventually, I was done:
In went the postcranial pair:
And pretty soon, you’d never have known anything had happened here.
Next time: exciting adventures with the badger head!
The pheasant comes apart
March 26, 2016
A couple of weeks ago, I was given a pheasant, which I reduced to science and food. When we last saw it, it was down to a skinned and partially defleshed head/neck and feet. It’s been through a couple of defleshing rounds since then, and today I was able to take it fully apart:
At the moment, the bits are laid out on this plate, drying. Small amounts of soft-tissue remain (and more on the second foot), which may need the attentions of invertebrates to fully clean.
It pains me to admit, but even though I have kept the cervical vertebrae, for most people the skull will be the interesting part. Here it is in a little more detail, disarticulated into about ten units. The mandible is to the right of this image; the rostrum to the left of it, and the main cranial section to the left again:
To the sides are the bones that laterally connect the rostrum to the braincase: zygomatics, quadrates and what have you. They are laid out roughly in the right positions, though the two quadrates may have been switched. Once everything is clean and dry, I’ll glue it back together, using my ostrich skull to help guide me.
The feet are trickier. Here’s the one I took apart:
At the top of the photo, you see a mass of ossified tendons, which operated the toes from more proximal areas. This is how all bird feet work, and it’s such a great scheme that it seems weird everything doesn’t do it.
Below these, we have the tarsometatarsus to the right, and the four digits to the left. Each digit has its phalanges in the right order, but I don’t know what order the digits themselves should be in. To help me get that right, I pulled out of prepping the other foot down, hence its current semi-zombified state:
I’m hoping it’s still intact enough to guide me as a reassemble the bones of the other foot. (Once that’s done, I may also take this one to completion, or I may decide that one pheasant foot is enough.)
Anyway, it’s nice to be progressing this specimen. Next, I need to figure out the best way to decapitate a medium-sized mammal (like a fox or badger) without damaging the skull, and using no special equipment.
I’m trying to free some space in my office, and I’m going to let my run of the Journal of Vertebrate Paleontology go:
It covers everything from 25(4) to volume 29(2) — a run from December 2005 to March 2009) — and also includes the lone issue 29(4) for December 2009 and the SVP meeting abstract volumes for 2006 and 2008 (i.e. issues 26(3s) and 28(3s)). (I don’t know what happened to the 2007 and 2009 SVP abstract volumes, sorry.)
All in all, they make a stack about 25 cm tall, and weigh just a little short of 17 kg.
Does anyone want them? Let me know within a week if you do. You either come and pick them up yourself from our home in the Forest of Dean, or pay for me to send them to you by your preferred method.
If no-one wants them within a week, they’re going in the bin.
(Note to self: size of package: 33x25x27)
Help me! How can I deflesh a tortoise?
March 22, 2016
I’ve been lucky enough to acquire another beautiful specimen. It arrived in a box (though not from Amazon, despite what the box itself might suggest):
What’s inside?
Can it be? It is!
Now I’ve wanted a tortoise for a long time, because they are (Darren will back me up here) the freakiest of all tetrapods. Their scapulae and coracoids have somehow migrated inside their rib-cages (which bear the shell), and their dorsal vertebrae are fused to the shell all along its upper midline. Just ridiculous. Look, this is what I’m talking about. Compare with the much saner approach that armadillos use to having a shell.
Here’s my baby in left anterodorsolateral view:
And in right posteodorsolateral:
Can anyone tell me what species I have here?
Here he is (or she?) upside down, in left posteroventolateral view.
Come to think of it, can anyone tell me the sex of my specimen?
Here he or she is in anterior view, looking very stern.
The problem is — and I can’t quite believe this never occurred to me until I had a tortoise of my own — how on earth do you deflesh such a creature? I have no idea (and obviously no experience). Any hints?
The European Commission is putting together a Commission Expert Group to provide advice about the development and implementation of open science policy in Europe. It will be known as the Open Science Policy Platform (OSPP).
This is potentially excellent news. The OSPP’s primary goal is to “advise the Commission on how to further develop and practically implement open science policy”.
But there’s potentially a downside here. We can be sure that the legacy publishers will attempt to stuff the committee with their own people, just as they did with the Finch committee — and that, if they succeed, they will do everything they can to retard all forms of progress that hurt their bottom line, just as they did with the Finch committee.
Unfortunately, multinational corporations with £2 billion annual revenue and £762 million annual profit (see page 17 of Elsevier’s 2014 annual report) are very well positioned to dedicate resources to getting their people onto influential committees. Those of us without a spare £762 million to spend on marketing are at a huge operational disadvantage when it comes to influencing policy. Happily, though, we do have one important thing on our side: we’re right.
So we should do what we can to get genuinely progressive pro-open candidates onto the OSPP. I know of several people who have put themselves forward, and I am briefly describing them below (in the order I hear about their candidacy). I have publicly endorsed the first few, and will go on to endorse the others just as soon as I have a moment. If you know and admire these people, please consider leaving your own endorsement — it will help their case to be taken on to the OSPP.
Björn Brembs is a neuroscientist who has been a tireless advocate for open access, and open science more generally, for many years. He has particularly acute insights into the wastefulness of our present scholarly communication mechanisms. His candidacy is announced on his blog, and I left my endorsement as a comment.
Cameron Neylon falls into the needs-no-introduction category. Every time I’ve talked to him, I’ve come away better informed and wiser, thanks to his exhaustive knowledge and understanding of the issues surrounding openness: both the opportunities is presents, and the difficulties that slow our progress. His candidacy is announced on his blog, and I left my endorsement as a comment.
Chris Hartgerink is an active researcher in text and data mining, whose work has repeatedly been disrupted by impediments deliberately imposed by barrier-based publishers. He knows what it’s like on the ground in the content-mining wars. His candidacy is announced on his blog, and I left my endorsement as a comment.
Daniel Mietchen both practices and advocates openness at every stage in the scientific process, with a special focus on the use of Wikipedia and the ways its free content can be enhanced. Fittingly, his candidacy bid is itself a wiki page, and endorsements are invited on the corresponding discussion page.
Konrad Förstner develops open source software for reasearch, works on how to make analyses reproducible, promotes the use pf pre-print servers and creates generate open educational resources. His candidacy is announced on his blog, and I left my endorsement as a comment. [H/T Daniel Mietchen]
Finally (for now), Jenny Molloy, is the manager of Content Mine and co-ordinator of OKFN, the Open Knowledge Foundation. She has announced her candidacy on a mailing list, but doesn’t yet have a web-page about it, to my knowledge. I’ll update this page as soon as I hear that this has changed.
That’s it for now: get out there and endorse the candidates that you like!
Have I missed anyone? Let me know, and I’ll update this post.
Wild Proboscidea in Oklahoma
March 20, 2016
I’m just back from a 10-day research trip to Oklahoma. I’ll have more pictures to post soon, of all kinds of cool things. One of the most surprising and interesting things I discovered on the trip was Proboscidea – not the mammalian order of elephants and their relatives, but the genus of plants with wacky seed pods native to the Americas.
I say I “discovered” Proboscidea, but all I mean by that is that I became aware of their existence – a personal discovery rather than a scientific one. People have known about them for a long time, and indeed Native Americans have been using the plants and even semi-domesticating them for millennia. The plants have several common names, including “ram’s horn” and “unicorn plant”, but they appear to be most commonly referred to as “devil’s claws”, and that is the name they’re known by in the Oklahoma panhandle.
The weird horns on the seed pods are adapted to snag on the limbs of passing critters, especially large ungulates, and cling there. As the animals wander around, they spread the seeds by either shaking them out of the pods or crushing the pods underfoot. Either mechanism works – the seeds and the pods they grow in are both incredibly tough, and a lot of gardeners find that the seeds don’t germinate well unless they’ve been scarified or even cracked open like sunflower seeds. Or so the internet tells me. I don’t have any direct experience of growing Proboscidea yet, but from pods too damaged to make good souvenirs I collected a couple dozen seeds, which I will attempt to germinate later this spring.
I accidentally got some personal experience with their typical mode of dispersal. I collected a double handful of undamaged seed pods and passed most of them out to students on our field trip, saving only a couple back for myself. I put those two in the back seat of Rich Cifelli’s truck, on top of my coat. By dinnertime it was dark and I’d forgotten about them when I reached into the back seat to grab my coat. As I walked toward the camp, I felt something dragging on my pant leg – it was the two devil’s claws, which had gotten tangled with each other and with me when they’d fallen out of the truck. I’d stepped on one and cracked the tip off of one of its horns, but the other pod, shown here, was completely undamaged. The seed pods are essentially made of springy wood and it takes a lot to damage them. This one rode home in my carry-on luggage, with the horns held at a 90-degree angle to the pod by a stack of books.
I didn’t put any scale bars in these photos – I should have, despite their inherent dangers – but if you’re curious, this particular seed pod is almost exactly 12cm tall, wide, and long (~5 inches).
One final point – I assumed that the genus name Proboscidea referred to the obvious similarity of the dried seed pods’ horns to the tusks of mammoths. But some of the online sources I’ve seen suggest that the name relates to the proboscis shape of the green, unsplit pods. I’ll try to track down the original description to find out which interpretation is correct, but whatever the answer, it’s pretty interesting that the same part of the same plant can at different stages of development look like either an elephant’s trunk or its tusks.
If you’d like to read more about Proboscidea, the most complete source I’ve found online is this page by Wayne Armstrong at Palomar College – in particular check out the photos of green seed pods that have not yet split open, which looks like fat green beans. There’s more useful information on this page and in the comments on this one. If anyone knows of better sources, or has personal experience growing devil’s claws, please let me know in the comments.
Copying content is not the same as theft
March 15, 2016
This post shouldn’t need to be written, but apparently it does. In recent discussions of Sci-Hub, I still keep seeing people trot out idiot analogies where copying scientific papers is portrayed as the equivalent of stealing physical goods. A couple of examples:
Mickey: You want a pair of shoes go to the shoe store and buy them. Notice you have to buy them. You want to read an article either pay or go to the library and read it for free. Notice unlike shoes you can read it for free! What is so difficult about this concept?
— Our old friend Harvey Kane.
Or:
“It’s as if somehow stealing content is justifiable if it’s seen as expensive, and I find that surprising. It’s not as if you’d walk into a grocery store and feel vindicated about stealing an organic chocolate bar as long as you left the Kit Kat bar on the shelf.”
— Alicia Wise, Elsevier’s ironically titled “Director of Universal Access”.
It pains me to read the words of experienced and presumably knowledgeable people when they trot out such absolute nonsense. Digital goods (which are copied) are nothing like physical goods (which are given and taken).
This is not complicated.
Here are some of the differences:
- If you steal my shoes, I don’t have my shoes any more. If you copy my Brachiosaurus paper, I still have it.
- Only one person can steal my shoes. Any number can copy my Brachiosaurus paper.
- Everyone agrees that stealing is bad, but plenty of people think that copying is good.
(Regarding that last point, note that I am not at the moment taking a position either way on whether copying is good or bad; just recognising that its morality is much more open to debate than that of stealing.)
The “analogy” between copying of digital goods and theft of physical goods is so utterly broken, so absolutely devoid of a factual basis, and so very misleading, that when someone uses it there are only two possible reasons:
- They are so completely ignorant about these issues that their opinion is of literally no value.
- They are deliberately confusing the issue.
So: ignorance or malice. There are no other alternatives.
Here, then, is my request. Those of you who are opposed to Sci-Hub may well have valid points, and I am happy to hear them — after all, it took me seven posts before I finally figured out what my own position is. But stop making invalid points. All it does is weaken your argument, cheapen the whole debate, and make you look dumb.
When you pretend that copying is the same as stealing, you undermine your own position.
Sauropod Vertebra Picture of the Week 
