Work bitchin'

[Lt. Killer M]

OK, I've had it. I've really had it now. Really really really had it!
I am peeved, mad, pissed off, fed up to my back teeth! [:(!]


I have been working on a publication for the last two months. Actually, three publications, all three on one and the same dinosaur. One I prefer not to talk about, it is taxonomic nitpicking. One made the submission deadline (last Monday) by a whisker. The third was fucked over by a breakdown of my Word - Reference Manager integration. So I am busy trying to stitch it together until next Monday, a deadline extension the editor very kindly granted.

It is a publication on Computer Aided Engineering modeling of a dinosaur named Kentrosaurus aethiopicus (http://en.wikipedia.org/wiki/Kentrosaurus). Cool beast, with a spiky thagomizer (http://en.wikipedia.org/wiki/Thagomizer)and (probably) an attitude. And there the problems start!

There are two important publications out there about thagomizer use: Carpenter et al. 2005 (and why oh why do I have a tendency to mis-type him as Crapenter?????? You'll see...), who calculated with two methods the impact force of a Stegosaurus tail, and Arbour 2009 (http://www.plosone.org/article/comments/info%3Adoi%2F10.1371%2Fjournal.pone.0006738) (I love open access journals), who deals with the closely related anklyosaurs.

So I thought, OK, go the smart and useful way, use their methods so that the results are all comparable. Fine, I sit down and read through the maths in detail - and the Carpenter et al. 2005 thingy is replete with errors! The first I notice is that they divide the calculated force of 2.8 x 1000000000 dynes (WhoTF uses dynes????) by the area of the tail spike tip (0.28 sqcm) and get......
11.2 x 1000 N/sqcm.

erhm, what?

2.8 / 0.28 = 11.2??????? forget the zeros, they do not matter, but if I divide any percentage of 28 by any percentage of 28 I get a multiple of 1. Not 1.12. [:O]
[:0]
[xx(]

OK, easy to correct, the resulting pressure is only 9% of what they say. No matter, it still kills.


Next, they claim that Impulse divided by area is the pressure.

Say what? Impulse unit is Ns or kgm/s, and if divide that by sqm I get kg/ms - a pretty weird unit. What you need to do is divide the impulse by the time it acts in (stopping time), this gives a froce and that per area gives the pressure. Which is what Carpenter et al 2005 then do: they correctly calculate the force - and end the maths there. pressure is not calculated. [:O][:0][xx(] me hates badly reviewed papers! I emailed the lead author, and he asked me to email the co-authors, two physicists(!) - who thus far have failed to reply. Arseholes.


Next, they calculate joint torques from anorexic muscle reconstructions, which means that I have to do one as well and do all the later doohickey with two models, one that's good and one that sucks.

Now, to make matters worse, after I worked my ass off to structure my work to deliver comparable results, I find this:

The torques they calculate are F(muscle) x moment arm, and the moment arm is defined as the half width of the tail.

at the risk that this gets old:say what????? [:O]:eek:[:O]
Instead of using the center of the muscle they use the most outward point - thats about a doubling of the value. So ALL their stuff is doubly wrong - how am I supposed to run a sensitivity analysis of all versions of my data while making sure I apply their methods AND correcting all their mistakes?

OK, still doable, I just need to ask for another extension......

And then, five minutes ago, I trip over this:

http://www.civduelzone.com/forum/attachment.php?attachmentid=305&stc=1&d=1253277999

erhm, what now? why is the maximum width smaller than the total width? OK, it might be the half-width (mislabeled), which is the (wrong) moment arm. But then, why is it not half???? or do they want to tell me that the tail got thicker-thinner-thicker-thinner-thicker-thinner from front to back? So that the base of each segment was much narrower than the middle? :confused::confused::confused::confused:


Me, I've had it. I now must decide whether to include all this (i.e. write a 'Carpenter et al. suck' paper) or drop it all out - which leaves me with a lot of work I did for no gain, and with insufficient material for the paper.


AARGH!!!!!!!


[/rant]

[barbu1977]

Never ask bio guys to do real maths. ;)

Don't realy have time to review the physic part of what you are saying, but about the table, with the * at the end of the table, I think the maximum with at base refers to the plate/spike base and not the tail.

[Shabbaman]

Coincidentally, I've been at a course in which dynes were used in calculations this week. Madness.

[Lt. Killer M]

Never ask bio guys to do real maths. ;)


yeah, the two guys who did it were physicists.

Don't realy have time to review the physic part of what you are saying, but about the table, with the * at the end of the table, I think the maximum with at base refers to the plate/spike base and not the tail.

Yeah, maybe they forgot a *. But it still does not make sense that the max width of the basal segment (link A) is less than the width of link A.

Coincidentally, I've been at a course in which dynes were used in calculations this week. Madness.

pervert! :p

[akots]

You are just a bit too young. You'll get used to that type of crap, I see a dozen examples of it every day around.

IMO, just take it easy, breath deeply, walk away and write something good, really worth of your effort. And never do what others did, do something of your own which is better, more thoughtful, and gives the better presentation of your point. If you think they screwed it all up, ignore their papers, do not cite them or at least may be still cite but don't go too deep into discussions.

With regards to PLoS ONE, I have had a lot of bad experience with it. A number of publications get through which normally should not just because of crappy review system. I know, it is considered to be very good and has high impact factor but quality of material published there is frequently below certain journals with crappy reputation. IMO, if you are sending your data to traditional journal and decide to plain disregard PLoS ONE publications, it might be OK with many a reviewer, at least in my area.

I've looked through the PLoS paper and it looks pretty comprehensive to me but I have not read it and by no means, I'm no expert in neither physics or paleo. Besides, it is very long and boring with no clear summary.

Again repeating myself, I would not try to fish out somebody's shit from somebody else's publications and make your point trying to show they are wrong or made a mistake. This would just create you a miserable reputation and won't help you achieve anything in the long run. IMO, that would be waste of time. It might be a better idea to try and concentrate on creating something of your own which would seem to be flawless at least to you and to reviewers of course.

[Lt. Killer M]

yeah, akots, you are exactly right, I guess. Thank you very much for your long and detailed reply. Exactly what I needed to hear!

I really needed to vent, because an at the start positive topic was drifting more and more into either throwing away a lot of work or becoming a very negative nitpick, and as you point out the latter is utterly undesirable.

I wish I could avoid both papers, but there is the slight problem that ANYONE who hears 'Stegosaur' and 'thagomizer' automatically thinks of the Carpenter et al. paper, and that the PLOS ONE paper is so current that it is still freshly on everyone's mind. Worst of all, I can expect my publications to be sent to either Carpenter or Arbour's thesis supervisor for review. Ignoring them is not an option.

OTOH, both are very fair people, so I will simply describe my research, then cite their work and list the problem as an explanation why I do not compare. Should be fine.....


I garee that the Arbour article is quite boring. That's what you get for publishing a thesis part without any further editing ;) And yes, PLOSONE is a problematic journal. What field do you work in? In mine, I can hang most of the blame on the name of the responsible editor :(

[akots]

Yes, you can do that, there are only a handful of authors. In my case, and I've been through most of molecular stuff with emphasis on pharmacology, sometimes there are papers with 15 authors and they go through repetitive process of 3-4 comprehensive reviews, you really cannot blame anyone. It is just that somebody somewhere overlooked.

In the field I'm working, the most frustrating thing is when you cannot repeat the protocols because it is either complete fraud (yes, these things unfortunately happen quite frequently), or some technician or student messed up with description of experiments, or reviewers let it go without sufficient details to make it repeatable elsewhere. At least in your case, the evidence is there for everyone to see (in museum I presume) and you cannot forge that. [lol]

[Lt. Killer M]

yeah, that is most annoying! In my field, reviews tend to be much better than in field that are much larger and have huge commercial interests standing behind publications (e.g. studies on new medications). However, there seems to exist an attitude of 'anyone can do biomechanics', when even those who studied the shit do them wrong. This means that absolute non-experts get to review papers, than editors think there is no need to ask experts (e.g. physicists) to go through the maths, and then there is Paul Sereno..... and there, everything breaks down: Mr. S. has been known to fiddle with data until it fits his world view, but not necessarily the evidence. He is known to try to pass off other people's achievements as his, and I do not think that he can make a good editor.

BLEH!

now yes, I can actually go an measure the skeletons. it does not matter than Carpenter et al. 2005 is not reproducable (and correctable), because the skeleton is there. In Denver. Some 12 hours of air transport and $ 3.000,- away :( Curated by - guess whom...... Not that I think he would not grant access. But still it is a bit embarrassing to tell someone 'you published nonsense, so I gotta do it again, may I please have access?'.

:)

[Lt. Killer M]

it is done, the paper submitted. Including a "Note to reviewers and editors", stating the problems with the other papers and why I could not solve them (author no answer so far).

puh!

[Lt. Killer M]

well, this paper came back, along with both others, and a very friendly email by the ediotr saying: We're sorry, we received 3 times the page count overall that fits in the journal. So, please, tell us which paper to take on now, the others must wait for other people's works to be retracted or refused. Alternatively, please feel free to submit them elsewhere.... the most polite pre-revview refusal one can write. And I understand: a special volume is a volume, not volumes.

Anyways, I chose to re-submit this one and another one elsewhere. The ohter one is already accepted (YAY!), and this one has passed 'initial quality control'. So, writing at the top:

NOTE TO EDITORS AND REVIEWERS: Carpenter et al. is crap, thus ignored

did not do much harm with the editors :)