UPDATE 01/06/11 I’ve now submitted a modified version of this abstract. Many thanks to all who commented.
One of the many conferences I’m going to this year is a fairly big event. The abstract deadline also happens to be very soon too. So I thought I’d post a draft of my abstract here and see what peeps think.
Is my Latin correctly formed? What do you think? Here it is anyway…
Nullius in Calculo: On the Explicitness and Reproducibility of Cladistic Analyses
Author: Mounce, Ross C P
Abstract: The result of a cladistic analysis should be repeatable.
Yet I present here numerous examples of recent papers in which the results contained therein cannot be replicated, given only the content of the paper, supplementary materials and links. Barriers to study replication include (1) absence of requisite information, (2) typesetting errors, and even (3) author error. I argue that these problems, many of which are easily-spotted, should not be appearing in peer-review published papers with such regularity. I humbly suggest that reviewers and editors not only examine the words of papers, but also the underlying data and calculations: Nullius in Verba, Nullius in Calculo. Furthermore, I believe the reporting of phylogenetic analyses would greatly benefit from increased Standardization following community-agreed criteria c.f. MIAPA (Leebens-Mack et al, 2006), and data deposition in appropriate data archives specifically designed to accommodate phylogenetic data e.g. TreeBASE or MorphoBank. In addition to problems with reproducibility, I also detail problems with explicitness of method reporting. A detailed manual examination of over 300 recently published ILD tests provides evidence to suggest that method sections are rarely sufficiently explicit in their detail to exactly replicate the methods used to generate reported results. In particular I suggest that authors should be encouraged to explicitly state how ‘gaps’ are coded and treated, and which branch collapsing rules are followed in analyses. Different settings can and do generate different results, therefore all such important settings should be explicitly stated.
[end of abstract]
Some further comment:
Any feedback good/bad/indifferent would be much appreciated.
My supervisor has given it ‘the green light’ in principle, but obviously is keen for me to handle the topic delicately and sensitively
I’m not out to ‘name and shame’ individual errors with this – it’s the system that needs changing IMO, and I’ll do my damnedest to make that crystal clear when I give the talk.
I’d be pretty surprised if this abstract was rejected – I’ve got strong evidence including an accepted Nature paper demonstrating some of this. Would love to blog more about this but Nature’s embargo policy rather prevents/scares me from doing so! My last talk at a Systematics Association conference (below) went down a storm too, picking-up a special commendation from the judging panel for it’s “unscorable” uniqueness [I used a Prezi] so I can only hope this next one will be as successful.
I’ve been travelling rather a LOT in the last 6 weeks or so; Rhossili Bay, London, Edinburgh, Leicester, Barcelona, Cambridge. It’s so nice to be back in Bath for a bit again.
While the memories are still fresh I thought I’d write a short summary of what I’ve been doing -> so much to update on my CV!
April 16 – 21 in Rhossili Bay helping my supervisor (Matthew Wills) teach undergrads about ecology, experimental design and real fieldwork. The weather was absolutely “lush” as they say in Wales. The students were well-behaved and did some excellent projects while they were there – staying up til past 3am in some instances on the last night to finish off their presentations!
The only downside was the lack of mobile phone signal. It’s stressful to be without internet for so long!
The very next week (April 26 – 28) I flew up to Edinburgh for a PaleoDB short course. Congratulations are sincerely owed to the organisers, especially Al McGowan, for taking the time to arrange such a beneficial event. PaleoDB is an *excellent* free-to-use resource but I do wish it was more Open. I made no hesitation in pointing this out during discussions. I have since applied to become a contributing member of the database (application pending).
After Edinburgh, there was the small matter of a conference to attend
Progressive Palaeontology 2011 was ably hosted at Leicester University. I gave a well-received talk on my research, sneaking-in some data sharing advocacy at the end:
Best of all, one of my labmates Anne O’Connor won the Best Poster prize – w00t!
Next-up: a well deserved holiday in Barcelona sunshine. Beautiful beaches, bountiful cerveza, and amazing architecture. Lovely!
Inside the Sagrada Família
No rest for the wicked… on the 19th and 20th I attended a short course at EBI-Hinxton entitled ‘Linking Open Data in Biology using Ontologies and Literature Mining‘. Had a superlative 3 course dinner in St Catherine’s college (Cambridge University) on the Thursday night, and a further meal in The Eagle the next night.
You might reasonably ask – why is a palaeontologist interested in ontologies and text mining? Well, it’s simple really – this field is crying-out for these techniques to be applied, and I hope I’ll be one of the one’s there first to utilize these powerful techniques on palaeontological data. The pickings could be rich, if only we had Open linked knowledge infrastructure in place… I shall no doubt blog more in future on this topic.
tomorrow today I’ll be going to a London BioGeeks event. Really looking forward to finally meeting Mark Hahnel face to face for the first time. I really think his FigShare initiative is an excellent idea. I’ve supported it myself by adding a few bits of test data. Will no doubt add more in the future…
Needless to say, all this travelling has completely wiped-out my £200 BBSRC Travel Grant. Have applied for more grants to fund my trips to Belfast, Berlin, Brazil and Las Vegas later-on this year!
*fingers crossed* – for richer or poorer, it’s going to be an exciting year!
May 23rd, 2011 | Posted by Phylogenetics - (Comments Off on What is Palaeophylophenomics?)
[Back when this blog was first started, it was hosted on www.science3point0.com (now defunct), and it was called Palaeophylophenomics]
It’s a formerly was a Googlewhackblatt
2.) It’s a Portmantaeu word combining my principle research interests, namely: Palaeontology (UK spelling!), Phylogenetics, and Phenomics sensu O’Leary and Kaufman (2011).
3.) Basically a convenient, informative unique identifier for this new blog.
Love it? Hate it? Let me know in the comments…
O’Leary, M. A. & Kaufman, S. MorphoBank: phylophenomics in the ”cloud”. Cladistics (2011). URL http://dx.doi.org/10.1111/j.1096-0031.2011.00355.x.
I need a space to layout my thoughts in a longer form than Twitter or Facebook.
So I thought: “hey, why not start a blog?” -> TA-DA!
*Posts will be infrequent and sporadic both in tempo and topic
Many thanks to http://twitter.com/jezcope for the quick hands-on WordPress tutorial, and Mark Hahnel for suggesting I blog here.