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.)

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.

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.

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.

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!

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.)