Tuesday, 24 December 2013

EDGE - Evolutionarily Distinct and Globally Endangered

Joining FATE in the pantheon of conservation acronyms, EDGE stands for Evolutionarily Distinct and Globally Endangered. It is the focus of the EDGE of Existence project, “saving the world’s most extraordinary species”:

“The EDGE of Existence programme is the only global conservation initiative to focus specifically on threatened species that represent a significant amount of unique evolutionary history.

Using a scientific framework to identify the world’s most Evolutionarily Distinct and Globally Endangered (EDGE) species, the EDGE of Existence programme highlights and protects some of the weirdest and most wonderful species on the planet. EDGE species have few close relatives on the tree of life and are often extremely unusual in the way they look, live and behave, as well as in their genetic make-up. They represent a unique and irreplaceable part of the world’s natural heritage, yet an alarming proportion are currently sliding silently towards extinction unnoticed.”

EDGE species are on the edge, so EDGE is clear pre hoc.

h/t: The Infinite Monkey Cage podcast

Sunday, 22 December 2013

FAIR - Flowchart Analysis of Investigation Results

If you are trying to establish where the blame lies for an accident, you might make use of FAIR: Flowchart Analysis of Investigation Results.

"The FAiR® System (Flowchart Analysis of Investigation Results) is an innovative management tool for determining the nature of errors and enables management to assess levels of culpability and ensure appropriate remedial actions. … By focusing upon the individuals’ actions and intentions as opposed to the consequences the FAiR® System guides intervention choices so that an organization can ensure that any defences put in place to prevent recurrence can be tailored to maximize effectiveness from both a systems and human performance perspective."

Because this is an attempt to make the blame game fairer (and avoid blaming the driver/pilot just because theirs is normally the last mistake before a crash), I think that FAIR counts as a pre hoc acronym. FAiR® might also be the first registered trademark on ORCA. I’m not sure what the lower case i is about, though.

h/t: The Pod Delusion episode 212.

Monday, 16 December 2013

BADGERS - Building Analysis Datasets and Gathering Experience Returns for Security

Whilst researching yesterday’s second WOMBAT, I came across another acronym even more contrived that the first: BADGERS - Building Analysis Datasets and Gathering Experience Returns for Security - was the name given to the Second Open Workshop for the WOMBAT project. Given that badgers have some superficial similarities to wombats, being “short-legged, heavy set” animals of similar size, I think that you can retroactively fit a connection so this one’s a post hoc.

For their commitment to contrived acronyms, I think the WOMBAT team deserve the second Outstanding Contribution To Acronym Generation Or Notoriety (OCTAGON) award.

[NB. This is not the first BADGER in ORCA.]

Sunday, 15 December 2013

WOMBAT - Worldwide Observatory of Malicious Behaviors and Attack Threats

Animal acronyms are always popular and today we have another WOMBAT - Worldwide Observatory of Malicious Behaviors and Attack Threats. This is an EU project, so unlike the last WOMBAT, there is no Aussie connection.

I am not sure whether wombats (which have cubic poo, by the way) are particularly malicious or threatening, although the Wikipedia entry does note:

“Humans who accidentally find themselves in a fray with a wombat may find it best to scale a tree until the animal calms and leaves. Humans can receive puncture wounds from wombat claws, as well as bites. Startled wombats can also charge humans and bowl them over, with the attendant risks of broken bones from the fall.”

As they are herbivores, I think that such attacks are likely only when they feel threatened. The link becomes even more tenuous when you realise that the attacks concerning WOMBAT are cyberattacks:

“The WOMBAT project aims at providing new means to understand the existing and emerging threats that are targeting the Internet economy and the net citizens.”

I run a bioinformatics lab in Australia but I am yet to encounter any coding marsupials, so I am rating this one a definite ad hoc.

Saturday, 14 December 2013

WOMBAT - Work Observation Method By Activity Timing

Coming back closer to home geographically, WOMBAT - Work Observation Method By Activity Timing is another UNSW research project, this time round out of the Faculty of Medicine:

“The WOMBAT technique was developed to undertake direct observational studies of health professionals using a handheld computer tool, allowing observers to capture multi-dimensional aspects of work and communication patterns. WOMBAT automatically captures all time data related to tasks, as well as detailing interruptions to work and multi-tasking.”

The link between WOMBAT and its underlying meaning is clearly just the Australian connection, so I think that it only merits a post hoc classification. It probably has the cutest acronym logo to date, though!

Friday, 13 December 2013

LAMARC - Likelihood Analysis with Metropolis Algorithm using Random Coalescence

A post on the Evolution Directory (EvolDir) altered me to another classic bioinformatics acronym today: LAMARC - Likelihood Analysis with Metropolis Algorithm using Random Coalescence, which has just been updated to version 2.1.9.

“LAMARC is a program which estimates population-genetic parameters such as population size, population growth rate, recombination rate, and migration rates. It approximates a summation over all possible genealogies that could explain the observed sample, which may be sequence, SNP, microsatellite, or electrophoretic data. LAMARC and its sister program Migrate are successor programs to the older programs Coalesce, Fluctuate, and Recombine, which are no longer being supported. The programs are memory-intensive but can run effectively on workstations; we support a variety of operating systems.”

I was all prepared to leap straight in and award LAMARC the coveted pre hoc acronym category for contriving a domain-relevant acronym when I was somewhat halted in my tracks by this statement on the website:

“The LAMARC package is not in any immediate sense derived from the work of Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck(1744-1829). The similarity of names is mostly accidental. But all evolutionary biologists do owe him a debt. Lamarck is an unfairly maligned figure. In addition to being one of the greatest figures of invertebrate biology, he was one of the founders (with Buffon) of the theory of evolution, and the first to propose a mechanism for evolution. You may want to read more about his life and work.”

I am not entirely convinced that the similarity of the names can really be “mostly accidental”, even if that particular acronym did leap out at them once they had the keywords. Either way, the evolutionary link is clear and so, accident or not, I think this warrants a pre hoc rather than post hoc. (Now go and read up on Lamarck.)

More JABBA Awards at keithbradnam.com

Just a quick post to note that Keith Bradnam has a few more contrived bioinformatics algorithms at over at keithbradnam.com for another round of JABBA (Just Another Bogus Bioinformatics Acronym) awards. I’ll no doubt steal them for ORCA once a decent amount of time has passed! :op (Actually, they’ve been up for a couple of weeks already, I was just slow to spot them.)

Thursday, 12 December 2013

ADAN - prediction of protein-protein interAction of moDular domAiNs

The ADAN Database - prediction of protein-protein interAction of moDular domAiNs - breaks the rules, really, as it is not technically an acronym. To be honest, I am not really sure what it is but it seemed so contrived that it warranted an ORCA entry. To add to the confusion, I do not know what “Adan” (the word rather than the database) is nor its relevance to protein-protein interactions, which is one of my own research areas.

As the database seems to be hosted by Universidad Miguel Hernández in Spain, the only thing I can think is that it is a backronym homage to Spanish footballer, Antonio Adán!

h/t: Nico.

Tuesday, 10 December 2013

SPITFIRE - Southampton Partnership for Innovative Training of Future Investigators Researching the Environment

SPITFIRE is the Southampton Partnership for Innovative Training of Future Investigators Researching the Environment](http://projects.noc.ac.uk/spitfire/), which is a doctoral training partnership (i.e. PhD programme) run out of the University of Southampton. The Supermarine spitfire is a well-known World War II British fighter plane developed by the Supermarine Aviation Works at Southampton. SPITFIRE therefore rates as an elite pre hoc acronym - and an impressively contrived one, at that.

Monday, 9 December 2013

FATE - Future of Australia’s Threatened Ecosystems

FATE - Future of Australia’s Threatened Ecosystems - is a project somewhat linked to the last post, CREATE and for some time was also housed at University of New South Wales (UNSW) in Sydney, Australia. It has since moved to the University of Sydney and I am struggling to find much more about it. The best so far comes from the webpage of Peter Ampt at U. Sydney:

For the past 6 years I have managed the Future of Australia’s Threatened Ecosystems (FATE) Program which began at the Australian Museum, moved to UNSW and is now to Sydney University. It is the brainchild of Professor Mike Archer and aims to explore the sustainable use of native species and ecosystems to generate conservation benefits. FATE has concentrated on the management and commercial harvest of kangaroos including consumer attitudes to eating kangaroo meat, the opportunities and barriers to achieving conservation through sustainable use, the feasibility of the use on native mammals as pets and the potential of regional bio-energy strategies to drive improved natural resource management through native agroforestry.

Fate… the future… I think that deserves a pre hoc classification.

Sunday, 8 December 2013

CREATE - Coalition for Research into the Evolution of Australian Terrestrial Ecosystems

CREATE - the Coalition for Research into the Evolution of Australian Terrestrial Ecosystems is a foundation run by my faculty (Science) at the University of New South Wales:

The CREATE fund has been established to provide a focus for studies into the evolution of Australia’s Ecosystems, concentrating on the last 100 million years.

The main emphasis is on the lessons that can be learned from the past and how these can provide an understanding of the present and the key to our future.

I think that CREATE counts as ad hoc but given that the products of their research constitute a stream of explanatory problems for Creationists, perhaps it is an ironic backronym!

Thursday, 5 December 2013

COLBERT - Combined Operational Load-Bearing External Resistance Treadmill

COLBERT - the Combined Operational Load-Bearing External Resistance Treadmill - is the device used by astronauts on the International Space Station to keep fit. The NASA treadmill was originally called the T-2 but was renamed:

NASA selected the treadmill’s name after comedian and host Stephen Colbert of Comedy Central’s “The Colbert Report” took interest during the Node 3 naming census and urged his followers to post the name “Colbert,” which received the most entries.

The acronym was engineered to fit the initials in a kind of inverse post hoc fashion (where the relevance of the acronym is added after its construction). In fact, COLBERT represents a new class of acronym to ORCA: the "Backcronym". (It was the Backcronym wikipedia page where I came across COLBERT, in fact.)

Wednesday, 4 December 2013

ACHOO - Autosomal dominant Compelling Helio-Ophthalmic Outburst

ACHOO - Autosomal dominant Compelling Helio-Ophthalmic Outburst - syndrome is another name for Photic sneeze reflex. This is the condition that affects around a fifth to a third of the population in which stimuli such as bright lights trigger uncontrolled sneezing. (Also known as “sun sneezing”.)

According to the source from which I discovered ACHOO, the ABC Science Weekly Update, it is “a funny acronym invented by doctors to help them remember the essentials of the photic sneeze reflex!” Personally, I think that “Photic sneeze reflex” is clearer than “Autosomal dominant Compelling Helio-Ophthalmic Outburst”! I suspect they were just having a bit of fun but, either way, it gets the coveted pre hoc status for such a well-aligned (if somewhat over contrived) acronym. (It’s just a shame about the “dominant” bit, which, ironically is probably the most likely bit to be forgotten!)