Archive for April, 2010



Call for dinosaur papers

This isn’t usually my thing to put up very academic bits on the Musings, but as I’m involved I probably should this time. Corwin Sullivan and I will be joint editing a volume of dinosaur papers for the Chinese journal Vertebrata PalAsiatica and this is an announcement to ask for submissions. This has already gone out as an e-mail to a couple of groups so feel free to ignore it, if you’ve not seen it and are interested then carry on this way:

Continue reading ‘Call for dinosaur papers’

More odd melanism

I’ve muttered about melanism on here before and the other day at Beijing zoo I saw a nice, if unusual example that seemed worth showing. Black jaguars (like this one) and indeed leopards are pretty common in zoos and turn up in the wild from time to time, it doesn’t seem to be an especially rare mutation, or one that is especially detrimental (hence it keeps coming back). However, even the blackest of these cats typically still show the underlying pattern of spots or rosettes through the otherwise black coat.

In this case through there is a fairly clear and gradual transition from the black background on top to a paler and more naturally orange / golden to white on the belly, with the rosettes naturally sanding out better too. This is not something I’ve been before, and while the animal is hardly half-way between being melanistic and normal, it’s definitely not fully black either. Colour patterns and things like albinism and melanism (or even amelanism) are complex and a wide variety of mutants and variations are seen, but given the number of black leopards and jaguars I’ve seen over the years, this was a pleasant surprise to see.

Barriers to effective science communication

Jim Kirkland flagged up this interview with scientist turned film director Randy Olson which you can listen to here. Randy’s central tenet is that scientists are not very good communicators because they tend to try and express facts rather than tell stories that might engage people better – we can do substance, but not style.

To a degree, he has a point, people can always improve their skills and obviously I do think this area is important. However, I take a bit of umbrage with the idea that scientists are, de facto, bad communicators. Many are clearly not, and be definition the better ones often rise to the top – I can think of plenty who do or have done lots of good science communication. I can also think of plenty of others who I know are or could be great communicators but are not given the opportunity and that brings me to my central point here.

In my experiences and from what I have seen, there are far greater and more pervasive and profound problems than some (or even most) researchers being poor communicators. There is often a general or even specific lack of support for efforts in communication from whole departments and institutes, or even colleagues. You can find yourself actively dissuaded from taking time and effort towards sci comms. Even if not, then the sheer pressures that face many researchers mean that such considerations are relegated to the last thing to do of a very full and constantly growing list. When you couple that with the all too familiar stories of horrendous media handling of science (everything from terrible misunderstandings of absolute basics right through to fabrication of stories and deliberate misrepresentation of research) that puts a tremendous filter between the researcher and the public then is any of this a wonder?

Are scientists truly bad at communicating or just inhibited from being able to do so, and wary of a near hostile media, hide behind facts rather than let slip anything that could be misconstrued or spun out of context? Where are the funds to allow researchers to visit schools and amateur groups, where are the bursaries to let them take time off to write books or articles, where is the allotted time in their contracts to allow them to do this work? It is such a low priority that these provisions are rarely, if ever, made (and if they are out there, I’ve seen very little evidence of them).This is as much, if not far more, of a handicap than some being less good at communicating than they could be.

Guest post: sauropod diversity over time

Phil Mannion and his pet dino.

PhD student Phil Mannion guests this time out on the Musings. Phil works on sauropods and has just had a new paper published looking at their fossil record and diversity over time. Do they really reach a peak of diversity in the Jurassic, or is this just a bias from how complete the specimens are from that time? Read onto find out more:

Continue reading ‘Guest post: sauropod diversity over time’

Sensationalising nothing

In the UK papers at least, this story has been doing the rounds. A hunter in China has trapped something rather odd looking and instantly all kinds of stupid is being stated about it. Wild speculation doesn’t even seem to be least of what I’ve spotted. ‘Last of its kind’, ‘new species’, ‘unlike anything else’ and more. Most annoyingly, the Times lead with a headline ‘scientists baffled’.

This is just sensationalist nonsense and indeed, all but libellous. Read the story and they reveal that the thing is still where it was captured and has yet to be sent for researchers to view. And there are no quotes for any researchers anywhere, just the hunter who caught it. Obviously ‘scientists are apparently baffled by something they haven’t seen yet and may not even know exists’ would be an infinitely more accurate headline. Claiming ignorance of a third party is not really fair.

Of course once you cut out the wild speculation and look at the (limited) evidence things become much clearer. I’m no expert on Chinese mammals, but some things here are obvious and they demonstrate only the ignorance and credulity of the reporting, not the apparent and alleged bafflement of researchers. A decent mammalogist will probably identify this in second.

So what do we know? First off, this animal has mange or some horrid skin condition. Some fur remains, but mostly it’s gone and so too are the whiskers. The skin is in poor condition too, emphasising that this is likely a disease, not a natural pattern. It’s also from central China, though that as a statement doesn’t narrow the range down much, or the local climate / environment.

Well, there’s no scale bar, but the wire on the cage is thin and the general shape of the shot makes it look like a small animal, maybe 2-3 feet total length. It’s also probably a carnivoran of some kind, but not a cat (wrong face, and the claws are not retracted) and not an otter either (too long a face, no webbing). It’s probably not a dog of some kind either given that the hind legs look much longer than the fore (a good look at the teeth would really help sort this out).  The body looks too stocky for a typical small mustelid like a weasel or somesuch. This leaves us with larger things like badgers, or my current best guess, a binturong (since it’s the largest civet in China I can think of with round ears). (Late break, the Guardian happily savage much of this nonsense and suggest it’s a civet, and of course demonstarte that scientists are not baffled by actually asking one).

I could be quite wrong, and without my mammal books and more information it’s hard to be sure. None of the supposedly weird and wonderful characteristics make any sense. The kangaroo-like tail cannot be seen, and in any case a wide variety of animals have surprisingly bulky and muscular tails once the fur is missing (especially arboreal ones). The strange noises are probably the result of this being an unusual animal, that is seriously ill, being dumped in a small cage for people to stare at. Lots of even very common animals make odd noises when stressed.

Now, this might be a new species, it’s always possible. But it does look like a generalised carnivoran / mustelid even from a single, bad photo with limited ancillary information. I’ll be most surprised if this turns out to be anything unusual at all. The supposedly unique and bizarre features are noting of the kind and what can be seen all fits with what we know about Asian mammals in general.

So in short, someone who knows nothing about basic anatomy or living mammals (even less than me, imagine that) and cannot spot a catastrophic disease assumes that this is weird and wonderful and will baffle anyone else who sees it. Then sensationalises said non-information and profound ignorance into the *most read* story on the Times website. Ask someone with just a bit of biological knowledge and they’d point out just how unlikely this is to be anything new or exciting. It’s also depressingly familiar to the ‘sasquatch’ that turned out to be a mangy bear a years or so back, and the ‘monster’ that was just a dead raccoon – this has happened very publicly before. What’s more, I can pretty much guarantee that when this does turn out to be something really not very interesting, there will be no coverage of this at all, and if there is, (based on previous experience) this might well be blamed on those same ‘previously baffled’ scientists who now are spoiling the fun.

It’s easy to be overly critical of these things but it’s hard to see their value. Is this turns out to be new and interesting, great, there’s a story there. But even the most basic bit of actual journalism (i.e. asking someone who knows even a bit about mammals) would reveal just how unlikely this is. It’s simply a non-story. There’s no evidence beyond ignorance that it is anything odd or unusual and the information that is available suggests that it isn’t. Yet, it’s spun into the most amazing and unusual thing in years which will turn out to be a great new discovery.

Ask A Biologist, an appeal

Regular readers will know that in many ways, the Musings is my ‘second’ project for science communication with Ask A Biologist being my first (and I think) best effort to bring science to the public. For the half dozen of you who have missed it,this is a site where people can leave their biology based questions and a team of researchers from all over the world will pitch in and try to answer. There’s no middle man, no filter of journalists, precis, reviews or anything else, you ask us, we answer.

And really answer in some cases, discussions of detailed or intricate questions have run to days or weeks over dozens of posts. We seem to operate a less formal peer review with people correcting each others’ errors, discussing points of taxonomy and definitions, philosophy of science and more. It’s a great introduction to the workings of academia and all the while bringing first hand information and knowledge to those who want it.

I really set the site up as it was the kind of thing I wanted as a child. I could read my books and watch TV shows but there would always be unanswered questions that I wanted answers for and had no way of finding. My parents, teachers and books (despite their best efforts) couldn’t provide them and I was left frustrated. Now the internet solves that problem, but with such a multitude of sources it’s hard to know who to trust. One quick glance at Yahoo questions should be enough to put anyone off ever putting something up there, but you might not realise this. Science by popularity is not a good idea. So enter AAB.

However, the site is run on the goodwill of the researchers giving up their time to help out and inevitably, despite some start-up money from PalAss, funds were tight. That is behind us now, thanks to a series of new grants and AAB is set for a relaunch with numerous new features, it’s more user friendly, with better archives, new images, new sections and more. While we have answered nearly 2500 questions and had over half a million readers in the last few of years, we are only as good as the people who use us. In short, if we don’t get many questions, we can’t answer them.

Time then, to spread the word. We are having our official re-launch on the 19th of April. If you like science and like learning about science then this should be a site for you, to read, to ask questions, to help out. Whether you are an academic biologist, a student, a teacher, an interested amateur or a 5 year old who loves worms, then we can help (or you can help us). Please then, on the 19th spread the word. E-mail your friends and colleagues, put a post on your Blog, Twitter, FaceBook or whatever, let your local school know or whoever.

We want to help and we can help, so let us help.

Thanks,

Dave

And here’s some pretty banners and logos to help you:

And again, and again, and again. Getting rid of teeth.

Convergence and its importance has been covered on here before, with examples of structures being lost as well as gained or altered. One of the most striking examples is the loss of teeth in the ornithodirans (that is, pterosaurs and dinosaurs and a few others).

Teeth can of course be adapted to do all kinds of things, but they can be expensive to produce and maintain (energetically) and they are not always the best tool for a job (and in terms of pterosaurs and birds are relatively heavy structures too) so you can see why some clades might loose them. And loose them they do, pterosaurs did it at least twice (and perhaps three or four times depending on exactly which phylogeny you prefer) and in the theropods there are ceratosaurs, ornithomimosaurs, oviraptorosaurs and birds (themselves more than once) all producing toothless forms. I don’t think there are any toothless sauropods or ornithischians, but several clades of the latter at least gave up teeth in the premaxilla. It’s not quite the same thing, but you could argue that they at least lost teeth from the bones of one part of the skull, if not lost their teeth entirely. It’s quite a record – at least eight independent sets of tooth loss which for a clade that are often characterised as being toothy shows just how often, and how easily, teeth can be lost.

(And indeed that’s just ornithodires there are several other archosaur and reptile clades that produced toothless forms, most obviously of course, the tutles).

On ignoring ideas

Another run in or two with some internet ‘eccentrics’ has prompted me to consider the oft expounded idea that to ignore something makes you close minded / incapable of handling the ‘truth’ / not a proper (or good enough) scientist etc. When you do dismiss an idea near instantly, it’s easy to give that impression to an outsider, but I suspect the truth may come as a surprise both to them and even to those with a decent understanding of science or a particular field. It is often a time saver – you have to demonstrate that your idea is worthy of consideration and that demands an understanding of the problems at hand – and no serious researcher is going to bother wasting time explaining why elephants can’t fly, the moon is not a body of gas, or that you can’t achieve nuclear fission in a soup can. Other things might sound much more reasonable, but can be dismissed just as easily and as quickly.

Science is, almost by definition, the search for reliable answers. As such we don’t dismiss ideas lightly and researchers can be very open minded. Reading a few of the more obscure papers out there, or going to a conference to hear talks or even just speaking to researchers will quickly show you that some have ideas that, at best, can be considered ‘controversial’. Some ideas just will not die despite the lack or evidence for them, or the huge stack of evidence against them. That may not be open mindedness so much as misguided dogmatism, but any accusation of close mindedness is silly if directed at science in general, even if it *might* be applicable to an individual. However, what is generally the cause of the instant dismissal is one of three things.

Firstly, and most simply, is a lack of evidence. Coming forward with an assertion with nothing to support it at all can be fairly dismissed out of hand. No evidence, no dice. Alternatively, trying to revive an obviously incorrect or highly questionable idea with no *new* evidence is just as dead in the water. The idea has been tested and the evidence evaluated and found wanting. If you don’t bring something new (and preferably big, dramatic and unquestionable) to the table then don’t wonder why you get dismissed.

Secondly, there is the lack of appreciation for what a researcher might know. You might not realise why you idea must be wrong, or cannot be right and we do. We do tend to know a thing or two about science oddly enough. If we fail to explain it or at least direct you to the information that will, then we are at fault. However, you’ll still be wrong, and it’s not being close minded or incompetent on our part to know you are wrong before reaching the end of your opening sentence if you have the expertise to know.

Thirdly is the one that’s surprisingly close to the first, but I left it till last as it might be a surprise. You would be simply amazed at some of the ideas science has actually considered over the years. Some truly outrageous ideas, concepts, and hypotheses have actually be put forward quite seriously AND tested seriously and properly. You might think your idea is being ignored without proper consideration, but it’s already had proper consideration and found wanting and we are back to the first problem. No new evidence, the idea stays defunct.

I’m happy to dismiss the idea that bats or birds are the nearest relatives to pterosaurs for example, not only because of the wealth of information that I know about phylogenetics and taxonomy and the profound differences in morphology and evolutionary history between the three groups, but also because this idea was actually taken seriously for a while (admittedly a rather long time ago) and people went over the details and looked at their similarities and differences and concluded they could not be closely related. At first and indeed second glance this should be obviously incorrect and no more worth of serious consideration than say the idea that manatees and mudpuppies could be closely related because of a few very vague similarities in body plan and lifestyle. But someone actually sat down and cross referenced birds and pterosaurs and bats and pterosaurs to test this idea. It’s been done already. Done properly in the way good science should be done, and found wanting. It can therefore be dismissed.

Researchers are open to ideas, but if you are going to come up with something odd, make sure you have evidence for it, and make sure the evidence is solid and really do make sure it’s not already been disproved. You can try to accuse a dismissive response as being close minded, but the answer is instead likely to lie with your own ignorance. I don’t have to revaluate your ideas now when someone did it a century ago and noting since has provided any support for the idea. Science does move rather slowly, but it does move forwards, and starting at the front and assuming there is nothing behind it will not help your cause. It just demonstrates that people were open minded enough to consider it, it’s just that it’s wrong.

Missing out

Some months ago I wrote a post about the proliferation of scientific literature and how hard it is to keep up, even with a relatively specialised field. Regular readers will also be aware of my paper on theropod feeding behaviour where I explicitly talk about and review the evidence for gut contents in large bodied theropod dinosaurs.

Not surprisingly there are not many papers out there on the contents of predatory dinosaur stomachs. I read what I knew about. I check those papers that had cited classic works that looked relevant. I read the papers cited in those classic works that looked relevant. I read reviews and check their citations. I spoke to other colleagues about the project and showed them the manuscript, and still other people read the paper during review and I’ve had numerous discussions about it since.

A couple of days ago in a conversation about this, Hans Larsson directed me to a paper on tyrannosaur gut contents. It’s by a well known theropod worker, in a well known palaeontological journal and deal with exactly the right subject. It was a record of tyrannosaur specimen with the bones of another chewed-up animal in it’s stomach. Yet, not only had I not cited this paper in my project, but I had not read it and indeed was not even aware of it. (OK, I might have forgotten, but the tile is clear and unambiguous and was exactly what I was looking for, it’s unlikely).

This brings home to me, stronger than even I had realised, how easy it is to miss things. I went looking for this kind of thing and everything about this paper meant I should have found it and indeed found it very quickly, yet it slipped through the gaps of my net, and it seems, quite a few others. Not that I am blaming my co-author or colleagues, but no-one else seemed to notice that this was missing or suggested that I include it, suggesting that at least some of them didn’t know about it either. There is a ton of literature out there and even when searching for something specialised, in a fairly systematic way on a subject where the material should be relatively easily available, it can be overlooked, even by a number of people.

If you’re looking for a kind of resolution to this, there isn’t one really. I wish I’d spotted this and I wish I’d found the paper and been able to include it. It would have strengthened my position in the paper and now it won’t, for me personally that’s a shame, but I suspect it might also be for the original author. He really should have got some credit for this from me and hasn’t, nor (in the literature) can he. Still, it might make me more lenient in the future when I try to puzzle how something has reached the literature without citing some of my work that appears (to my eye) to be essential to the proposition. I hope it might also reach the ears of a few referees who can be more lenient themselves when castigating authors for having missed key papers. It can, and does, happen.

To praise, not to bury

Thanks to Linheraptor, Xixianykus and the feeding traces,I think I have been dealing directly more with the media in the last three weeks than the preceding three years. While it could be considered true that on occasion I might be less than impressed with the media coverage of science (and with good reason), I have also encountered a new raft of writers who have gone to the trouble of actually fact checking, asking for information, reading papers, communicating things accurately, not turning ‘maybes’ into ‘dids’ and more.

Of course, not everything written makes it into print and I’m aware of several stories that never made it. As such, some of the better things done by better people are not out there and I can’t link to them. This is especially ironic given that in a number of cases this appears to be becuase the editor didn’t think the story was good enough, despite the fact that dozens of other news outlets ran the story, typically by cribbing it from someone else and making it less accurate. Thanks.

Even so, some did make it and here are a few of them. Here. Here. And here.

The science network

A good scientist knows what he knows and knows what he does not know. He has a good idea of his strengths and weaknesses and his areas of expertise and ignorance.

I know I know pterosaurs and theropods quite well, sauropods less well, ornithischians much less well and so on. I have a good handle on systematics and taxonomy and behaviour, but not on taphonomy or morphometrics. However, crucially, I also know people who are good at the things I’m not good at and are not good at the things I am good at. There are also people who are real specialists and can use a method or know a group better than almost anyone else alive, or generalists (which I’m certainly closer to) who can do a fair range of things quite well and link the other stuff together. Together we have breadth and depth.

This is important for two different reasons. Firstly it allows us to cover both a wide range of fields and get deep into them, without us all tripping over each other’s work. People can specialise or generalise and science will move forward as a result. More importantly though, it allows us to cross check and revise our collective work and have confidence in what we are doing across the whole of science, even, or perhaps particularly, when we have little or no understanding of that field individually.

I really do not know very much about astrophysics (big surprise). But I know a couple of people who do. I know the training they go through, I know the colleagues they have who check and review their work (peer review) and examine their ideas in the literature (through papers). I also know that those people are also cross-examined and checked by still other people and so on. It would be enormously time consuming, but I bet I can find a chain of co-authors and collaborators that links me to my collegiate astrophysicists. I have collaborators in geology and biology and some of them will have collaborators who are chemists and biochemists and physicists right up to guys working on star formation. At every point each person will have anywhere from a handful to dozens or even hundreds of collaborators, and dozens or hundreds or even thousands more who are reading and reviewing and replying to their papers. They have enough expertise to analyse each link in the chain, and perhaps one or two links either side of it, even if they can’t begin to handle either end.

Sure, there’s no-one out there (I suspect) who knows as much as I do about a couple of specimens I’ve worked on, but there are people who know nearly as much, and who know more about other close specimens, and know more about the methods I used to test them. This constant cross checking and evaluation means that we can have real confidence in our results and methods. I may not know how the stats package on my computer runs an analysis I want to use, but I do know that the mechanics have been written and tested by software engineers, I know the stats concepts have been produced by mathematicians and the methods have been verified by others. There are biologists with enough maths background to check the principles behind it and the appropriateness of the methods and the correctness of the results and so on. I know the taxonomy of the group at hand is right because enough taxonomists have checked the principles used to erect the species and specialists on the clade have looked at the anatomy and ecology and confirmed the species are distinct and so on. They may not know each other or even recognise each other’s work (I suspect you could really confuse a mathematician with a graptolite and some whale baleen), but it all fits together.

In this sense then, scientists are not so much a group of individuals as a cohesive whole. There are, obviously, errors made (occasionally profound ones) but this colossal network of research ideas and analysis does produce a singular, and generally very reliable, whole. I may not understand astrophysics, but I recognise and trust the methods used to generate the data, the analyses and the people behind it. So can you.


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