China 2014 part 1

My colleague Michael Pittman is a young, ambitious and smart researcher who has done some very nice work on tail stiffness in archosaurs. Now, Michael has a grant going for a project that expands on his previous work, and there are a lot of big names on the grant along with him – and I am on it as well! Not because I am one of the bigshots (most certainly not), nor because I know much about tail stiffness in archosaurs, but because I can build nice research 3D models in a variety of programs, including the necessary 3D digitizing. Previously, I collected data at the AMNH for this project. And in February it took me to China two weeks ago.

Michael and I wanted to check out some fossils in this place: the famous IVPP.

china_01
Pics taken from my hotel room; the XiYuan hotel is a very good place to stay and IVPP visitors get a very reasonable rate.

The IVPP is a research institute, and I’ll have some thing to say on that topic later, but it also has a museum part. For reasons that will become apparent in due course my visit to that museum was rather short and somewhat strenuous, and I have little to write and show. Let’s get this over with, and then advance from the holiday part of my trip to the work aspects.

In the center of the main room of the IVPP museum there is a big pit that houses a number of dinosaur mounts. Here’s a hapless Tuojiangosaurus multispinus having a very bad day at the hands… erh, teeth of Monolophosaurs jiangi (thanks, Dave Hone: I forgot to take a pic of the label of the latter dinosaur, but your photo of the two mounts includes it).

IVPP_02

Of more interest to me, given my history of involvement with plateosaurid dinosaurs, is this critter below: Lufengosaurus!

IVPP_03

OK, looks rather clumsy. The dinosaur below is much nicer:

IVPP_04

Sinornithosaurus millenii. Fluffy! :) It was really cool to see this really famous specimen.

Now, work. What took me to China this year was Michael’s rather cool project on oviraptor tails. But as I happened to be at the IVPP anyway, and as my esteemed colleague Jingmai O’Connor had suggested that I give a talk on photogrammetry there, and as there actually was a time window that allowed me to give that talk, and as my famous colleague Xu Xing at the IVPP actually managed to arrange things……

IVPP_01

… I did give a quick intro to a rapid and cheap 3D-digitizing technique. The announcement, above the one that hung in the elevator, suffered a bit from being copied from what I jotted down for Xu, who apparently had some trouble reading my admittedly horrible handwriting. But the presentation was a success, with the listeners (palaeontologists and archaeologists alike) becoming increasingly interested instead of nodding off to sleep – always a good sign!

Michael and I studied a number of specimens I can’t show you, because they are not on exhibit, but I can show you one that is on exhibit in the National Geological Museum (homepage if you read Chinese) in Beijing. The specimen is labelled Shenzhousaurus orientalis NGMC 97-4-002, and it is shown in a glass-covered steel-cornered box. Very safe, which is good. Although I hate when exhibits are behind glass because it makes seeing and especially photographing them so much harder, it is much better to have them behind glass than damaged or stolen. And too many museums, the NHM London and the MfN included, have had dinosaurs on exhibit pawed and fingered and broken by the unwashed masses. In this case, I would have done things a tiny bit different with regards to the lighting, but then, I always have photography and photogrammetry on my mind, whereas museum exhibit planners have other priorities, mainly the dramatic impact.

Shenzhou01

Shenzhousaurus orientalis type specimen with calipers for scale. Note the blueish light stemming from a neon tube mounted inside the glass cabinet.

So, I set to photographing this small precious raptor, which was a bit of a bother because of an unfortunate meeting of my left knee with the Beijing sidewalk asphalt the day before (the reason why my IVPP museum visit was not that much fun, and short). Suffice to say that I felt very House-ish limping through Beijing and through the Geological Museum (a place well worth an extensive visit!) on my crutch. I was, however, capable of handling my camera and tripod quite well. Here’s a glimpse at the results of ~5 minutes of photography.

geol inst

As you cannot see in this screenshot, the model came out quite nicely, although not quite perfect. I blame the dust on the inside of the glass for some imperfections – and I can’t get rid of that horrible colour!

 

 

 

Posted in "Prosauropoda", Dinopics, Dinosauria, Hadrosauridae, IVPP, Ornithischa, Sauropodomorpha, Theropoda, Travels | Leave a comment

A wonderful Plateosaurus drawing

Currently, I am horribly busy and thus not able to blog much. But here I have something that I must show you, now that I have finally managed to scan it.

PlateoDrawing
click for larger size

Last fall I received this wonderful drawing of a Plateosaurus stealing my birthday cake from none other than Himmapaan (Niroot Puttapitat), a exceptionally gifted (and extremely diligent and thorough!) artist – find more of his work here on his blog and here on deviantART, or here on Facebook. He is also a very modest and friendly person, as I found out when I had the pleasure for visiting the London Zoo with him.

As you can see, the Plateosaurus above is not only properly muscled and proportioned (and appropriately bipedal), but also meticulously drawn in tiny detail. Oh, and the dragonfly that tries to hide away on the top left is gorgeous, too! Every time I look at this wonderful picture I can’t pull away and study the minute details afresh.

What a wonderful present – thank you very much, Niroot! It gives me great joy every time I see it!

Posted in "Prosauropoda", Dinopics, Dinosauria, Plateosaurus, Sauropodomorpha | 4 Comments

Photogrammetry tutorial 6: building a model from the photos

We’ve been through the details on how to take photos for photogrammetry (parts 1, 2, 3, 4, 5), now it is time to talk about the next step: how to actually get a program to build a model for you.

For all those who wonder why there are no pics in this post – patience, young Palaeowan! There will very soon be a paper out that has all the info and pics you need, and that’s all I will say now :)

There are plenty of photogrammetry programs out there (see this overview, somewhat incomplete, on wikipedia), some of them for free, some of them looks like they cost nothing, and some that cost money.

Why do I say some ‘look like they cost nothing’? Because some cloud-based programs actually do not cost money, but want the copyright to your models, and some even to the photographs you upload. Quote from Autodesk 123D Terms of Service: “… you grant to us and our affiliates a world-wide, royalty-free, fully paid-up, perpetual, non-exclusive, transferable, and fully sublicensable (through multiple tiers) right and license (but not the obligation) to reproduce, distribute, redistribute, modify, translate, adapt, prepare derivative works of, display, perform (each publicly or otherwise) and otherwise use all or part of Your Content, by any and all means and through any media and formats now known or hereafter discovered, but solely in connection with the Service and/or our business activities (such as, without limitation, for promoting and marketing the Service) and/or to comply with legal or technical requirements.” Obviously, they need rights to do much of that so they can actually use your raw data to make a model for you, but look at the bolded parts! Imagine you create a really neat model of something, and Autodesk distributed printed-out copies of it as an advertising gift to millions of people……. That’s a minefield you should NOT get into!

Personally, I use Agisoft’s Photoscan Pro. An educational license costs $549, and the program covers 99% of my needs, while being extremely user-friendly. Also, I have made excellent experiences with the Agisoft support team, via their user forum, so overall I am very happy with my choice. Others tell me that the professional Autodesk program Image Modeler  is excellent, too, and it contains a lot more than photogrammetry capabilities. On the other hand, VisualSFM (SFM = Structure from Motion) is completely free for personal, non-profit or academic use, and gives you many options for handling difficult data sets that Photoscan Pro doesn’t have. My esteemed colleague Peter Falkingham is a great fan, and has used it successfully for some very neat science work, including the reconstruction of the Paluxy River trackways from old photos. Peter also has a neat guide on how to use VisualSFM and the free mesh editor Meshlab up on Academia.edu, so if you’re registered there, go grab it.

So what you read below is what I do in Photoscan, and if you use a different program you may need to adjust things a bit to the specifics of that program. The general principles, however, hold true for all of them.

Alignment and Model Building

Before I give you details on what to do in-program, it is important to know what kind of raw data set you have, as directions differ a bit.

Immobile specimens

If we’re dealing with an object that you could only photograph using the walk-around method, you should simply throw all the photos into one Chunk in the program, and run Alignment*. If the resulting sparse point cloud (a point cloud consisting of all the points the program used to find the camera positions) and camera positions look fine, the next step is generating a dense point cloud. You now have two options: have the program build it, then clean it up by removing the objects around your specimen, or mask all photographs to remove the objects around your specimen, and then have the dense cloud calculated. Usually, the former is more difficult, while the latter takes longer. If I need to do a lot of pre-alignment masking, or if I want to be very sure that the final model will have perfect edges where the real specimen contacts its support, I opt for masking first. Otherwise, I often choose middle ground: I mask all photographs, but only where the specimen contacts the ground. That gives a nice distance there, to use for cropping the dense point cloud.

* Remember that if there is motion in the background, like people walking through, you will need to mask the moving objects on all photographs they appear on!

So, decide how to proceed, mask as necessary, align the photos (Menu ‘Workflow’, option ‘Align Photos’). Now adapt the selection box as needed (sometimes, the auto suggestion will cut off part of the specimen), and have a dense cloud built (Menu ‘Workflow’, option ‘Build Dense Cloud’). Crop that dense cloud as needed and have a mesh built (Menu ‘Workflow’, option ‘Build Mesh’)

Turntable specimens

If you used a turntable for the photography, you will likely have to mask the background in all images. And I assume that you took at least two sets of photos, between which you flipped the specimen over so that you can get a model of the underside, too.

In this case, you can proceed as above, with prior masking or with cropping-after-dense-cloud generation if you treat both series separately, and only combine them into one chunk later (what I term the multi-chunk method; see below on how to do that). However, the most elegant way is having all photos in one chunk, and having Photoscan spit out the complete model in one go. This I call the one-chunk method.

For the one-chunk method, you should always mask all images. If you made sure that the background in your images is out of focus or so blank that Photoscan can’t find any points, it may be enough to mask the ground below the specimen near the contact points – but that may lead to colour errors in the final model. Thus, I recommend spending the time to completely mask the background in all images. Luckily, Photoscan has an ‘invert’ option for the masking tool, so you can simply click the masking line all around the specimen, hit the invert icon, and then ‘mask’.

Now align and see – if your photos are good you should get a perfect alignment! Build the dense cloud, the mesh, scale it (see below) and enjoy! Yes, that simple!

If it is that simple, why would anyone use any other method at all? Well, the one-chunk method has one slight drawback: it depends on you taking really good photographs, that are perfectly suited for photogrammetry, and taking them in proportion to the part of  the surface they show. If Photoscan has a hard time finding enough points in some images, or if there are parts of the surface that are grossly overrepresented in the images, you will end up with a sub-perfect alignment. Or if you can’t really fill the frame of the image with your specimen, which is not that rare when you digitize small specimens with a normal lens. In really bad cases, Photoscan may even be hard pressed to align the photos from one set, and there are ways for helping the program along, mostly using the background for alignment. However, if you do that, you need to have the background immobile versus the specimen (i.e., rotate it with the turntable, e.g. by placing a printed text page on the turntable and under the specimen), and you can’t use the one-chunk method easily.

For the multi-chunk method, which you can also use if you did not use a turntable,you must place each set of images in a chunk of its own. You do NOT want to mask the background that moved with the specimen. However, you should mask a thin strip around the specimen, to create a small gap in the dense cloud that makes cropping the background away easier. Basically, it is the same thing you want to do as with immobile specimens. Now, align the photos in each chunk, check the alignment, create the dense clouds, and delete the background points.

Next come the tricky part: you need to place at least three markers on each model that are in the exact same spots on both chunks. The best way is to place those markers on the photographs by finding a point that you can really nail down to the exact pixel on several shots, right-click on one photo on it, choose ‘Create Marker’, then right-click and ‘rename’ that marker (e.g., ‘A’ or a speaking name like ‘large sand grain on left postzygapophysis’, or whatever). If the marker is not perfectly located you can left-click and drag it.

Now, go to another image from the same set that shows this point, right-click on it, and choose ‘Place Marker’. From the pull-down menu, choose the correct marker. Repeat this procedure until you have three markers placed and visible on the dense cloud, and check that they show up on the cloud where they should be.  This is a good check on how good the alignment within each chunk really is. If your markers aren’t in the right place on the cloud, check your makers on the photos. If that’s all OK, you can’t use photo-based markers and need to switch over to cloud-based ones. These you create similarly, but it is all a bit more cumbersome, as you can’t right-click a marker to rename it, nor can you shift its position with the mouse. And later it will mean that you can’t merge the two dense point clouds into one, but have to calculate a new one from the merged chunks’ sparse point cloud – ugh! So do try to find images that are well-aligned and create your markers on them.

Now, place markers in the exact same places in the other chunk, and rename them to the exact(!) same names. Now, choose ‘Align Chunks’ from the workflow menu, set the method to ‘Marker based’, make sure the correct chunks are selected, and clikc ‘OK’. There is an option that is a bit confusingly names ‘Fix Scale’. It does not, as I first assumed, fix any scale differences between the chunks, but rather makes Photoscan NOT scale the chunks to fit each other. DUH!

Once aligned, you now need to merge the chunks. Menu ‘Workflow’ –> ‘Merge Chunks’. Logically. As I said, Photoscan is very user friendly ;) It creates now a new chunk, so your previous work is untouched. You will want to merge the models, so tick that box. Do NOT tick the box for merging markers, as un-merged markers are an easy way of spotting problems. Now, check out the merged dense cloud in the new chunk. If the marker pairs are very close together and the cloud looks fine, have a mesh generated and you’re done. If something big is amiss, it is usually caused by erroneous marker placement. Delete the merged chunk and fix, then align the chunks anew and merge them again until satisfied.

Scaling the Model

This last step should be easy, provided you followed the protocol and added a scale. All you have to do is mark the ends of your scale in at least two photos. In Photoscan, you right-click in that place on the photo, choose ‘Create marker’, and then rename it (e.g., 0 cm or 3.7 cm or whatever; it is usually smart to use a speaking name!). Then, choose another point and create a second marker, and rename it (e.g., 10 cm or 7.2 cm). Try to use the longest distance between markers you can find!

Now, go to another image and find the same points. Right-click, choose ‘Place marker’, and select the correct marker. Doing so in one other image will do, and you do not even have to create and place the two markers in one image each. You can place one marker in, say, your 5th image, another in your 8th, and place the first on image 3 and the second on image 11. Doesn’t matter, as long as the scale object you used hasn’t move relative to the specimen between all those photos.

Once you have the two markers, select them both (CTRL and left-click one, then the other), right-click and choose ‘create scale bar’. Switch to the Ground Control tab (at the bottom left!), select the scale bar and enter the length for it. CAUTION: Photoscan is in meters! Now, click on the ‘Update’ icon on the top of the pane (it looks like two blue arrows forming a circle). DONE!

 

 

 

Posted in Digitizing, photogrammetry | 1 Comment

Adolf “Dolf” Seilacher, the Grand Old Man of trace fossil analysis, has died

Last week, one of (or arguably the) greatest palaeoichnologist, Adolf Seilacher, died at the age of 89. I met him only rarely, and had little professional interaction with him, but that little makes me mourn his death more than I would mourn most other colleagues, even many that I worked or work with closely.

When I was a young student goofing off at Tübingen University I was lucky to have many excellent professors, luminaries in their field. Adolf Seilacher, however, stuck out in many ways, although he was rarely present: “Seili”, as German students called him behind his back, had retired before I even enrolled, but like many of his colleagues he would never stop being a researcher and teacher. Although he spent much time on Yale and in the field, he usually taught a compact course in Tübingen every second summer, and one year I was able to attend. The course was on trace fossils, Seilacher’s main research area, but instead of “Trace fossil analysis” (or whatever the actual German title was), it should have been called “How to be a good scientist, on the example of trace fossils” or some such.

I’ll have some more to say about this course later, but first let me tell you about Seili as a person. From spring through fall, everybody in the building always was aware of his arrival, because he invariably arrived on his trust old Vespa. I do not know how many he owned in succession, but given the work-out he gave them there must have been many. Over the course of the trace fossil analysis course and various conversations I had with him over the years there were quite a few stories, all research-related, that included “mei Veschpa” (yes, he had quite a Swabian accent). It all started, I gather, when as a young grad student or freshly promoted doctor he did not have the means to travel by car to sample the Pyrenees for trace fossils. So he packed as few personal effects as possible, loaded his Vespa with himself, his wife and a backpack that “threatened to work as an involuntary friction brake on the rear tyre”, as he put it, and set off. The narration was accompanied by a hilarious pantomime of the vehicles leaning on slopes up and down. As with many other stories, I am sure some embellishment was involved – but as I came to realise very quickly the embellishments were never meant to increase Seili’s prestige, but rather to drive home the lesson more forcefully, usually via humour. All of these lessons, and nearly every story had one, were delivered with boyish enthusiasm and twinkling eyes, had little to do with being a conforming scientist, and more with being an independent, active, diligent and resourceful inquisitive person. Much, however, was often left unsaid, and it could take me a while to figure out what exactly the central message was.

The funniest and certainly weirdest story Seilacher told us was that of a field trip to the deserts of western Egypt during which a neighbouring research camp was raided by Libyans, who abducted a young American researcher. The poor man was quickly and unceremoniously set free again at the door of some US embassy in Northern Africa, IIRC, and Seilacher thought no more of it for a few years. Then, he was accosted at a conference by a young man he had never met before, as far as he could recall, who stepped up to him and said words to the effect of “great talk – by the way, you’re the man who got me abducted!” It turned out that the Libyans had intended to abduct the world-famous Yale & Tübingen professor, and by accident driven to the wrong camp, abducting an insignificant PhD student instead of Seilacher. Seili concluded the story by remarking dryly that this encounter made him think twice about the personal invitation letter from Muammar Ghaddafi for a research stay in Libya! Needless to say, he didn’t go.

Another story, one that he repeated twice during the one-week trace fossil course (which already tells you that its lesson is important) was that of another meeting with a colleague at a conference, who tore into Seilacher’s just-given talk on trace fossils from some site in Jordan or Morocco or so (sorry, the message got across so well that I forgot the details). The colleague informed Seili that he had been to the very same rock exposure the summer before and had found plenty of trilobite body fossils, which Seilacher said didn’t occur there, but nary a one of the trilobite traces (Cruzianas) that Seili had talked about. He must, insisted the colleague, have mixed up the cliffs and formations! Seili, on the other hand, was quite adamant that yes, he was quite able to read a map, thank you very much, and that he was quite sure of the place and formation. The two of them parted with the conflict unresolved, but with an agreement that would allow a solution to be found a while later: that they would meet there and check out the place together. When they actually managed to make the joint field work happen, they found that they had indeed been talking about the same place. Now, one went left, the other right, to hunt for fossils. Thirty minutes later them met again. Unsurprisingly, Seilacher’s backpack was full of trace fossils. However, his colleague had a backpack full of trilobites! Having seen each other’s spoils, they now changed sides – and golly, the place was indeed full of both body fossils and traces! Lesson learned: collection bias is much stronger than even the most experienced researchers will be ready to believe!

Seili had many idiosyncrasies that make for great story-telling, foremost that one could never know if he was being serious, or making an important point in an elaborate way – or simply pulling one’s leg! A certain playfulness and sense of humour also pervaded his scientific work, most notably expressed in some of the species epithets he coined. Asteriacites gugelhupf is a track made by a suspension feeder from the Carboniferous of Egypt, the bilobed scratch pattern of the upturned arms suggests an asteroid rather than a brittlestar. Seilacher named the trace, because of its similarity in shape, after a cake that is a favourite for birthdays in Germany. Such names that were driven by everyday connotations and associations crop up quite often in his works, as well as other versions of “speaking names”. To Seilacher, science and everyday life were not separated, but one, and while some may see some of his work as science outreach, to him it was just natural, and communicating science to non-scientists came natural to him.

Others way more qualified than I will have much to say about Seilacher’s scientific work, his impact on palaeontology and ichnology, his Crafoord Prize and so on. I’ll just quickly note a huge part of his life effort that falls squarely within the outreach category, and has had a profound impact on the perception of palaeoichnology: the Fossil Art exhibition. This travelling exhibition takes casts of trace fossils and presents them as if they were works of art – accompanied by short texts succinctly explaining what they are. The overall presentation always has the character of an art exhibit, and Seilacher and his collaborator, Tübingen preparator (or should I say preparation magician?) Hans Luginsland selected mostly specimens with an immedatie artistic appeal. The latest version of the catalogue book for the exhibition is available in German from Schweizbart. You can find (low quality) photographs and details on many of its panels it on this page that accompanied a previous stop in Denmark. The most famous one, I guess is this one with plenty of Cruziana on it.

The show has travelled world-wide, with the last two stops in 2013 having been the ETH Zurich and the Senckenberg satellite in Dresden. As far as I could ascertain, the show has now been gifted to Senckenberg, but I was unable to find out where it will move next. I hope the death of Adolf Seilacher will not result in it being stored and forgotten, as it is a beautiful and striking way of arousing interest for palaeontology, and a branch often ignored and unknown to many at that, in the general public, fascination people of all ages and backgrounds.

But now it is really time to come back to the one Seilacher course I took. Trace Fossil Analysis was held in the summer break, with the lecture hall in the main building of the Institute of Geosciences in Tübingen stifling hot or, windows open, noisy and hot, quickly creating a drowsy atmosphere. Still, most attendants were highly motivated, as was the lecturer. We quickly went through some charismatic and historically important trace fossils, including Hitchcock’s ‘birds’ and, obviously, the Chirotherium story. Then came the first invertebrate tracks, and for some tedium set in. And Seilacher proved to be as excellent a lecturer as I had heard: he’s explain things repeatedly, until everbody had had ample chance to understand things, but didn’t mind that some of the quicker minds blanked out after the second repetition. So once he moved on to the next topic, he always raised his voice slightly to ‘wake’ us all again, before he proceeded, with a smile, with the next weird traces. Sometimes, he could hardly keep from laughing when suddenly, people sat back up who had lain down across several seats while he had been talking with his back turned.

At the end of the course, he gave each of us a trace fossil to comment on, as an oral exam. Given the large number of failures and successes he had seen during his long career, it was very touching to see how he tried very hard to coax a modicum of coherently presented knowledge out of the least gifted and interested, so that he could pass them and give them the coveted “Schein” (Attendance Certificate; grades were irrelevant as they didn’t count into the final grade for the diploma), and how tensely he waited for the replies from the obviously smart and interested – as well as his relief when they did perform well. Seili really cared for every young student who attended, and he understood the strength, weaknesses and motivations of all of them!

Let me end this post before I now get all maudlin. Seilacher will be greatly missed by many colleagues, as the many facebook posts already show. I hope that his legacy lives on in the works of the many students and colleagues he influenced.

 

 

 

 

 

Posted in ichnofossil, Palaeoart, sad news, Tübingen | 5 Comments

Taylor & Franics misrepresents DFG guidelines on Open Access – an innocent error?

Thursday, April 17, 2014, I received an email from Vicky Gardner of Taylor&Francis (tandf.co.uk) inviting me to participate in a survey regarding Open Access Mandates. Here’s the email’s text:

Dear Heinrich Mallison,

Tell us what you know for a chance to win $100 Amazon voucher

We are currently surveying our European authors with a mini-survey about Open Access mandates from funders, in specific countries, both inside and outside the European Union.

After picking your country, the survey will display a summary of the relevant mandate and four short questions, plus one extended question:

https://www.surveymonkey.com/s.aspx?sm=DkhsZZgxin2l3a2bKuKR2A_3d_3d

Enter the survey before 30 April 2014 for the chance to Win a $100 Amazon voucher.

Taking this survey will allow us to find out how authors think these mandates will impact their work. The results will be shared with the global research community and EU policy makers, helping to inform and influence the debate on open access.

Kind regards,

Vicky Gardner, Open Access Publisher
Taylor & Francis

There was also a link to opt-out of further messages, but that’s not relevant to the topic of this post. Also, I find it quite interesting that they feel it is necessary to repeat that Amazon voucher thingy, and bold it each time. But let’s cut to the chase here: What would you say the survey is about? Specifically, what mandates is it about?

“After picking your country, the survey will display a summary of the relevant mandate

That sounds, at least to me, as if they will show me the mandate that in Germany applies to authors in general – after all the email says “our European authors”.

Is there anything hinting at the mandate in question being some obscure special case for very limited special programs? Or does it sound as if the survey deals with the run-of-the-mill standard mandates any average author will encounter most of the times he/she decides to publish Open Access? To me, it is clearly the latter.

Now, I clicked the link, got taken to a site where I selected “Germany”, and was then shown this:

TandF_01

let me enlarge the relevant parts in a more blog-format-friendly manner:

TandF_02

So, what do they claim?
– that they give a summary of the relevant policies for researchers in Germany, specifically the DFG’s Gold and Green Open Access policy.
– implicit in this claim is that said policy applies to “funded researchers”, and by the absence of any qualifiers they make it sound as if that means by and large every DFG-funded researcher in Germany
– that the policy mandates that researchers choosing Green Open Access must deposit their article in a repository within 6-12 months, depending on the discipline they work in
– that the policy mandates publishing Gold Open Access only in journals in which ALL articles are available for no fee.
– and that the policy in reverse mandates that researchers may not publish Gold Open Access in journals that have a for-pay or other option to make only selected articles available free of charge.

The latter category of journals encompasses a vast number of very prestigious journals, like Biology Letters and other Royal Society journals, Journal of Paleontology and Paleobiology, or journals that fall under T&F’s very own open access rules, such as the Journal of Systematic Palaeontology. PLOS ONE, Palaeontologia Electronica or Fossil Record, where every article is freely available (in case of PLOS ONE and FR the author must pay, PE does not charge a fee), are not affected by the mandate.

So, is this true and correct?

And the answer is a resounding NO!

T&F is kind enough to provide, on the website, a link to the document that details the policy they “summarized”. And “summarize” they did, but……

TandF_03

WHOA! What does it say there? What exactly?

“The programme enables research universities to obtain funding from the DFG which they can use to finance the publication fees charged by open access journals.”

OK, that is an issue for researchers: if your university applied for and received funding under this program, and if you want to use that funding to pay for your Open Access fee, then you must comply with this policy. But that’s only one small part of the story of Open Access publishing by German researchers! Most people I know use the publication funding that comes straight from their project, under point 2.6 of the guidelines for Regular grants, which is a separate and totally unrelated programme. And here’s where I must come to the defence of T&F, involuntarily. Section 2.6 of the guidelines for a regular Sachbeihilfe (Regular grant) in English only reads
“2.6 Project-related publication expenses
Please state whether you wish to apply for publication funds and if so, the amount. In conclusion, state the total sum of requested funding for direct project costs.”

However, the German version is much longer, and roughly translates to

“2.6 Project-related publication expenses
a) as a subsidy to publication of scientific project results funds up to 750.- € per year of project duration can be made available and used for freely selected publication venues (but not for “grey literature”).
b) …..
c) ….”

Here’s the full thing, note that b) and c) deal with book publications.

TandF_04

So you see that maybe, just maybe, we must excuse T&F for totally missing out on an important point here. Assuming that they have nobody capable of checking the DFG website and translating the longer and obviously more detailed German version of the guidelines. Maybe. Considering that T&F is a huge publishing outfit I seriously doubt they do not have anyone handy who is capable of checking the rules properly. But hey, who knows?

Be that as it may, the simple fact remains that the Regular Grant guidelines do not place any limitations regarding Open Access journals on how you spend the publication funds. None at all!

Now, is that the only source of direct funding to a researcher for publication funding? No, you can also apply separately from your project. Guidelines for that programme are here: http://www.dfg.de/formulare/51_10/51_10_de.pdf. And I can tell you that there is no mention of any Open Access policy in that document. None! At! All!

So what is the issue here? It is the simple fact that point 2.6 of the guidelines for a regular grant, the point that very many people get some serious money  (2250 € for a typical project) for publication cost from, does not, in any part, specify anything about a policy on Open Access publishing! Zero, zip, zilch! The DFG simply does NOT, in any way, impose ANY limitations on how you spend the money, as long as you spend it for proper scientific publishing (i.e., with peer review).

So T&F presents a sole policy as “what [...] funded researchers have to do”, as the “relevant mandate”, a policy that does not apply to regular cases, to the primary source of funding researchers use for publishing, nor the after-the-project extra funding application. They do not mention the regular case of normal, run-of-the-mill projects at all, but by chance(?) happen to present a special case as the norm! And, by that “pure accident”, T&F choose to present a quite restrictive policy, instead of the rather lenient non-policy that let’s you pretty much do whatever you want with the money, provided it goes out for publication.

An innocent mistake? Somehow, I am smelling a rat, a big, fat weeks-dead rat!

UPDATE: the DFG has a big web page on “OpenAccess and the DFG”, so to speak: link in German and link in English. Takes a bit of navigating to find the exact answer to the question which mandates (if any) cover specific cases, but a very good start.

Posted in Open Access, Open Access publishing | Leave a comment

Photogrammetry tutorial 5: a little visual aid for you

Here’s a little video I cooked up to show the turntable photography method I described in part 3 of this series. I do not wish to part with the dough to buy the video update for WordPress, so please find the file in a download here. It needs renaming to tutorial.zip, then you can un-zip the file and watch the video. AGAIN: you must rename the file so that the ending is ZIP, not PPT!

Teaser images:

034 markers scale_bar

Posted in Digitizing, photogrammetry | 2 Comments

Holding hands with Plateosaurus

Although I did not start my professional career in palaeontology as a dinosaur researcher, but (can you believe it?) as a palaeobotanist, the Upper Triassic basal sauropodomorph dinosaur Plateosaurus engelhardti from Central Europe has been accompanying me for a very long time. When I started my studies of geology/palaeontology at the University of Tübingen, two mounted skeletons stood in a second floor hall of the institute, which triples as a lecture hall, office and museum building. These mounts, erected under the direction of Friedrich von Huene, still stand there today, although (thanks to a new curator) the room looks much nicer: the window had been bricked over, but has by now been restored.

Sauriersaal_Tue_rechts_sm

One of the two skeletons, GPIT/RE/7288 on the right, later became the guinea pig for my doctoral thesis. However, although it is beautifully preserved and nearly complete individual, some parts of the skeleton were replaced for my digital range of motion studied with parts of the other skeleton, informally known as ‘GPIT Skelett 2‘ (on the left). This included the hand, because the left hand of ‘Skelett 2’ is in very good condition compared to the left hand of GPIT/RE/7288. Because the two skeletons are of nearly equal size (in fact, the three skeletons are; ‘Skelett 2’ is a composite made from two individuals), the mixing of the bones was not a problem. However, although many elements of the hands of GPIT/RE/7288 are preserved, I decided to use the complete left hand and lower arm of ‘Skelett 2’ in one piece, so that any problems that might arise from the bones stemming from different individuals would be limited to one joint, and not mess up the wrist of metacarpus.

The bones were all CT-scanned at the University Hospital of Tübingen University, by the very helpful Dr. Ludescher, and I extracted the 3D shapes in long nights at the museum, mainly spent waiting for the computer and hoping it wouldn’t crash again. Comparing those extractions to similar work today just serves to show me how old I am: computers have become so incredibly much faster and have so much more memory that, although I have witnessed the process, I can scarcely believe it.

The resulting files were the basis of my two ‘Digital Plateosaurus’ publications in PE and APP, as well as my thesis. During that work, I limited myself to analyses of the skeletal range of motion that dealt with the big questions of posture (bipedal or quadrupedal) and major limb and body motions. I took quick peeks at foot posture and hand function, but didn’t do detailed analyses, as I did not feel competent to do so. That the manus was mainly a grasping or digging organ, and did not play a significant role in locomotion, was obvious to me from the simple fact that both I and, a short time earlier, Bonnan and Senter (2007) had found that Plateosaurus was incapable of sufficient pronation (turning the palm down) to walk on its hands, and thus had to have been a biped. My modelling of the centre of mass (a line of research that I am still pursuing, see my latest paper in Fossil Record) showed that Plateosaurus was well balanced as a biped, and a bit of whimsical whole-skeleton posing showed that a quadrupedal posture looked rather ridiculous.

Plateo_pose

From here: Virtual skeleton of GPIT/RE/7288 in quadrupedal poses in lateral view. 1: Digitigrade, 2: semi-plantigrade, 3: plantigrade hindlimb. 4: as 3, but with vertically positioned femur at midstance. 5: equal limb length posture. Length of left femur is 595 mm.

However, a tiny bit of nagging doubt always remained: I knew that there was a lot of cartilage in dinosaur skeletons, much more than in mammals, and what if I had been wrong about the pronation issue because of that?

Skip ahead a few years. I had been busy with other work, but the Plateosaurus hands and feet were still on my mind. And then an opportunity presented itself to come back to one of these issues and do a detailed study of the hand’s ability to support the animal’s weight, or grasp things. A student in Bonn at the Steinmann-Institute, Stefan Reiss, was looking for a diploma thesis topic, and willing to undertake the gruesome task of modelling the Plateosaurus manus.

Stefan dug right in, although we faced a number of challenges. First of all, the spatial separation between Berlin and Bonn, second, the fact that he had to try and serve two masters (me for the computer aided engineering modelling work and Martin Sander in Bonn as the official supervisor of his thesis work and for the palaeontological aspects), third a long and arduous variety to computer problems – it all conspired to make the work more difficult. However, in the end Stefan got things done, and received his diploma. I’ll spare you the ugly details how we managed to coax the data out of the PC, using a software for which support was yanked out from under our feet (don’t you hate commercial programs?) during the study.

Next step, obviously, was publishing the results. Again, things proved difficult. I can today laud Stefan for improving his English a lot while writing his thesis and the paper, but at times I wanted to find all his former English teachers to give them a stern talking-to. Also, because the program had run out of license, as it was not sold any more, we couldn’t happily go and create figures any way we wanted, but had to live with what had accumulated for the thesis. Stefan quickly learned how to handle the Computer Aided Design and the Computer Aided Engineering program, and started out on a series of experiments that I will only partly describe here – namely, as far as they are included in the current paper.

We had decided early on that the paper would go to PE – after all, PE is open access and asks no fees, neither from readers nor authors. That’s because of the funds provided by PE’s sponsors and because of the many volunteers who work for the journal, which includes me in the function of style editor. Unlimited colour figures, unlimited length, a lack of false pretence about the “importance” of the journal and whether the paper is “important” enough – what more can you ask? Thus, off to PE the paper went (and no, I have no influence whatsoever on the editorial process).

In the end, as is often the case, the review process proved very helpful, even though it was a tiny bit frustrating. I sometimes complain that reviewers should not ask that authors “write a different paper”, and for good reason: a reviewer’s job it to check on what you did do, and how you present it, not what you might have done differently for the last six months or two years, if you had back when you started known where your research would take you, and what the personal whims of the reviewer are. In this case, however, the reviewer didn’t suggest that we toss our existing paper, but rather that we re-think the entire publication strategy. He suggested that we cut the paper in half, with the first half being what you can now read in PE. The second half, he said, should be expanded with lots of additional work, and then published as a second paper. And this approach makes a lot of sense: Stefan gets a paper published now, a paper that isn’t too long and over-complex, and we also get to publish the rest of his work, albeit later and after some serious time and money investment. However, that second paper will then really rock!

So we decided not to fight, but to accept this review, and adapted our manuscript as suggested. It now is narrowly focussed on the question: Does the hand of Plateosaurus show a range of motion and robustness compatible with regular use during locomotion? And the answer is a resounding NO! The third finger is long and flexible enough to have been used in locomotion, but it alone is far too weak to carry a significant part of the animal’s weight. The second finger could share the load, but both together are still a far cry from sufficient support. The other fingers are too short, and/or weak, and/or too immobile. What’s more, the pattern of mobility doesn’t fit together, so that the forces would not be properly distributed between the fingers. But, quite the reverse: the fingers turned out to be very good as flexing, thus grasping things!

(What must be kept in mind is that “locomotion” doesn’t mean taking tiny shuffling steps while feeding, but actually going places – sustained change of location. Nobody is saying that the hand couldn’t be used as a prop while the animal was drinking or feeding from the ground.)

cross sections

Digitigrade or not? Preuschoft’s method in action on the hind limb of Plateosaurus. The cross sections of the bones above and below the ankle joint that were involved in carrying the animal’s weight (tibia+fibula; metatarsals II-IV) are nearly equal, indicating a digitigrade posture.

Additionally, we used a smart method Prof. Preuschoft once taught me to calculate the relative strength of the metatarsus and lower arm in comparison. If an animal walks in a digitigrade posture, i.e. with only the toes touching the ground, it is reasonable to assume that the sections of the limb are roughly equally robust, because they are under roughly similar loading regimes. Obviously, it plays a role how much weight really is on them: the thigh doesn’t carry the load of rest of the limb it is part of. Also, what angular excursions occur? The bigger the angles the higher the bending loads. But neighbouring elements in the distal limb should see roughly similar regimes. Thus, the cross sections of tibia+fibula (close to the distal end, but not at the articular ends, where shapes are also defined by the necessities of the joint) and the metatarsals should be roughly equal. If, on the other hand, the animal is plantigrade, a big part of the weight is carried on the heel, and the metatarsals can be slimmer. Preuschoft tested his theory on the hands of monkey, some of which walked in digitigrade posture, some in plantigrade, and the results matched the predictions. (sorry, I have lost the reference – oops!) So we did the same thing for Plateosaurus, forelimb and hind limb (data on the latter not in the paper, so see figure above) and guess what: the hind limb indicates a digitigrade posture, but the much shorter forelimbs indicates plantigrady! So, the limb that is too short anyway is further shortened in its functional length by being forced into a platigrade position? That makes no sense whatsoever.

In all, what Stefan showed in our paper is more nails in the already sealed shut coffin of plateosaur quadrupedality. The other part of your combined work, the part that we’re holding back for the next paper, will be more positive, telling us about what the animal could do, not what it couldn’t. That’s always more fun, but also usually more speculative. It will take us a while, though.

My thanks go to Stefan, logically, as well as to Martin Sander and the entire PE team. It is a pleasure to publish in a completely free (no author fee, no reader fee), i.e. true open access journal. I am also very grateful for the two reviews by Matteo Belvedere and Matthew Bonnan! Although one of them gave me quite a head-ache and made us totally re-vamp the paper, both reviews were fair, to the point, and very helpful.

 

Posted in "Prosauropoda", 3D modeling, anatomy, Biomechanics, classic CAD, Digitizing, Dinopics, Dinosauria, locomotion, Navel gazing, Open Access, papers, Plateosaurus, Sauropodomorpha, Tübingen | Leave a comment