The Ant Room

E. O. Wilson working on a novel

2008-07-15T23:45:00.003-04:00

Apparently, he would write a novel.

In a recent article in the New York Times, E. O. Wilson is said to be working on his first novel:

"Over lunch he describes his novel in progress, currently titled “Anthill.” Its contents have occasioned certain differences of emphasis between himself and his publisher, even though it was his editor at Norton, Robert Weil, who suggested he write it. Dr. Wilson would like ants to play a large role in the novel, given all the useful lessons that can be drawn from their behavior. The publisher sees a larger role for people and a smaller, at most ant-sized, role for ants. The novel is rotating through draft after draft as this tension is worked out."

I can't wait to read it.

Primary vs. Secondary forest

2008-07-07T16:00:00.005-04:00

Photo: Tiputini Biodiversity Station -- tower view

It occurs to me that I am not doing a good job of living up to my blog mission statement. More specifically, I have not been "keeping track (for my own benefit) of my daily progress in the identification of the ant fauna of Tiputini Biodiversity Station in Ecuador, the analysis of that data, and the pursuit of my PhD." To remedy that situation, I shall tell you what I am doing right now.

Right now I am working on a paper comparing ant diversity in primary vs. secondary forest. This is from a small pilot study Amy Mertl and I did in 2002. It was our first visit to Tiputini, our first field season, and our first attempt at identifying ants. We were not very good. We would sit together in the lab, one of us with a key and the other at the microscope. We had never heard of pinning so we just looked at them in alcohol. We had never heard of Bolton, so we used the key in The Ants. One of us would read through the key couplet by couplet and the other one would say things like, "I guess the first one" or "what the hell does that mean?" or "is there a third option?" or "why don't you take a look." And no one was around to tell us if we got anything right (or wrong). It's a miracle we got anything right at all. Of course, the beauty of keeping your ants in alcohol is that you can go back and re-identify them. :)

Interested in how biodiversity is affected when primary forest is cut down and then allowed to regrow? There is an interesting article in a recent issue of Science on rainforest biodiversity in recovering forests. Check it out here.

Ant #3 (Tim): wood burned ant trail

2008-06-30T14:59:00.005-04:00

This lovely trail of ants was created using a wood burning pen on a very small piece of wood (about 1 cm wide).

My Tiputini Mantis Database: The Numbers

2008-06-25T08:00:00.000-04:00

9: # of subfamilies.

64: # of valid genera records.

17: # of genera represented by a single species.

110: # of species represented by a single specimen.

65: # of species represented by two specimens.

10: # of species represented by over 100 specimens.

8483: # of specimen records.

50: # of species records for the genus Pheidole, the most species-rich genus in my collection.

65: # of Pheidole species Amy Mertl has collected at Tiputini.

154: # of Pheidole species on John Longino's Ants of Costa Rica website.

14: # of people (besides myself) who have helped me to identify species.

70: # of specimen records for specimens that are definitely not ants.

8: # of years I have been in graduate school.

6: # of years that have passed since I collected my first specimen at Tiputini.

27: # of copies of various versions of my database that I have.

5: # of places I keep backup versions of current database.

29: # of specimen records that contain the phrase "lost specimen" in the specimen notes.

861: # of specimen records for reproductives.

108: # of specimens that I was unable to identify to anything more than "Formicidae"

542: # of species records -- this includes fake ones like Formicidae (Formicidae) where I know it's an ant but have no idea what kind it is or Attini (Attini) where I know it is an Attine, but have no idea what kind. It also includes the classic Hymenoptera (Hymenoptera), otherwise known as "it has six legs and wings."

503: # of species records -- this does not include the above fake species but does include morphospecies and new species, and is not necessarily the number of species that I have collected, as it includes certain morphospecies which may overlap each other.

???: # of species I have collected.

Ant #2 (Kari): Bitstrip Ant

2008-06-20T09:00:00.001-04:00

This ant was created on Bitstrips, which is a pretty cool site that lets you design characters and create comics very easily. It was mashed together using silhouettes of baseball bats, lemons, bottles, a heart, and two golf tees. I forgot the antennae, though.

An ant a day (ish)

2008-06-19T08:00:00.000-04:00

I've been a big fan of the skull-a-day blog where the author created a new piece of art (with a skull theme) every day for a year. I thought, I can do that! And (obviously) I would want to use ants as a theme. I made a deal with my husband that we would take turns making something every other day and I would post the results in this blog. Turns out we are both pretty lazy and have come up with nothing close to an ant a day. More like an ant every couple of weeks. I will still post the results here, though. We also make no claims as to the quality of the art -- it's just for fun.

Day 1 (Tim): bent wire ant

International Code of Area Nomenclature (ICAN)

2008-06-18T06:06:00.002-04:00

John S. Wilkins over at Evolving Thoughts pointed me in the direction of a new code which has just been published in the Journal of Biogeography that aims to standardize the naming of areas of endemism and other biogeographical areas. This new code would be similar in scope to the International Code of Zoological Nomenclature (ICZN), which governs how we name new taxa. The smallest area would be named a district, followed by province, dominion, region, and realm. From the abstract:

"Biogeography needs a standard, coherent nomenclature. Currently, in biogeography,
the same name is used for different areas of biological endemism, and one area of endemism is known by more than one name, which leads to conflict and confusion. The name ‘Mediterranean’, for example, may mean different things to different people – all or part of the sea, or the land in and around it. This results in ambiguity concerning the meaning of names and, more importantly, may lead to conflicts between inferences based on different aspects of a given name. We propose the International Code of Area Nomenclature (ICAN), a naming system that can be used to classify newly coined or existing names based on a standard. When fully implemented, the ICAN will improve communication among biogeographers, systematists, ecologists and conservation biologists."

Apparently someone has already published a paper which utilizes this new system. López et al. (2008) includes the following statement from the abstract:

"The following zoogeographic provinces are proposed for Argentine freshwater fish fauna following the International Code of Area Nomenclature: Andean Cuyan, Patagonian, Aymaran, Great Rivers and Pampean. The former two are placed within the Andean Subregion of the Austral Region, and the latter three within the Neotropical Subregion of the Holotropical Region. These provinces, based on results coinciding with PAE and cluster analysis, represent the first classification of Argentine provinces based on objective methods."

There are a lot of reasons why I'm doing what I'm doing and one of them is that I like organizing systems. They make me happy. I like putting things into categories and (theoretically) bringing order to chaos. At its best it feels like the "after" photo from one of those articles about organizing your closet. Look how clean and organized it is now! Every sock has its own little cubbyhole, sorted by color and length. Summer outfits on the left, Winter on the right. Shoes all lined up and ready to compare to your purses so you can color coordinate your outfits! Considering a new dress? Now you can easily and efficiently scan all the dresses you already own, and be able to make a good decision about whether that new dress is really all that different from all your old dresses! Isn't it wonderful? Won't life be so much better now? Just think of all the time and money you will save!

So you can see why this new system seems pretty neato to me. I have certainly run into problems in the past trying to figure out what exactly people are talking about when it comes to geography. Or what term I should be using for my area of study. Western Amazonian lowland rainforest? Yasuní region? Upper Napo region? Amazon Basin? Lowland Ecuadorian rainforest? Yasuni National Park? Tiputini Biodiversity Station? The Neotropics? It is not always clear to me.

On the other hand, it is also not clear to me how exactly I would utilize this new code in reality. Perhaps there is a list somewhere of currently accepted terms, but if so, I can't find it. So does that mean that everyone is starting from scratch? I don't even know what a realm is. And I would think that all of these areas would be attached to particular taxa. For instance the areas of endemism for freshwater fish are probably not going to be the same as the areas of endemism for ants or birds. At least at the province level. But they would certainly overlap. At the top of the hierarchy, though, they might be the same. How does that work? You can cite previous work, so I could (for instance) cite Bolton and divide ants into the classic groups of Nearctic, Palearctic, Neotropical, Afrotropical, etc.), but would those be kingdoms? Realms? Districts? Would the Neotropical region for ants be different from the Neotropical region for freshwater fish? How would my newly defined areas fit into the existing system? Or is there no system yet? I'm not clear. Perhaps some concrete examples would help me understand it. Of course, I've only spent about an hour browsing the internet to figure this stuff out, so all the answers could already be out there. But I really need to get back to work!

And now for something fun -- Elements!

2008-06-17T08:05:00.000-04:00

The return of the ant room maven

2008-06-17T08:00:00.000-04:00

As some of you may have noticed, I have been absent on this blog for quite awhile now. The reasons are various and sundry but mostly involve the fact that I discovered some major problems with my master database and I think I have been going through the 5 stages of grieving:

Denial -- I'm sure this isn't that bad. Maybe just a couple of records gone awry. I'll just check my email first.... My desk is so disorganized. I'm going to clean out my desk so I can have a good environment to work in. Yeah, I really should figure out what is wrong with my database. But I think I'm coming down with a cold. Probably better if I take the day off and rest so I don't get really sick. It's important to take care of yourself! I will definitely deal with that whole database issue tomorrow.

Anger -- #@!!%!!!!!!!

Bargaining -- Perhaps I have some older version of the database that isn't messed up. Hmmm... not on my computer... maybe on one of these twelve million random disks that are sitting in my desk. No... maybe on my old laptop that died four years ago. Okay, that doesn't work. Perhaps I should spend several days making my old computer try to work. That seems reasonable. And so on.

Depression -- Everything is bad... (groan).... I'm going to have to re-identify every... single... specimen... (moan).... I'm just going to curl up in a little ball for awhile....

Acceptance -- Okay. I really just can't trust my database anymore. The only way to be sure of the data is to do a pin-by-pin inventory of every single specimen in my collection and match them up to its record in the database. If I don't see it in front of me (and I didn't send it off to another researcher) then it doesn't exist.

So that is what I have been doing. Which is a process both boring and stressful, the worst possible combination. The good news is, I am now officially done. HURRAY!

A really useful blog post (not mine)

2008-04-14T18:17:00.003-04:00

Photos of L. humile and some other species by Alex Wild

Alex Wild over at Myrmecos has just posted a really useful post on how to identify the Argentine ant, Linepithema humile. I wish I'd had this post back when I was identifying all my samples. I cannot explain to you how long I agonized over whether I even had Linepithema, let alone which species they were. This is such a nice explanation that I may even be motivated to go back and look at some of those specimens again. Ack!

Brachymyrmex

2008-04-01T09:30:00.000-04:00

Brachymyrmex is one of those genera that is really easy (for me, anyway) to identify to genus, but almost impossible to identify to species. The only species I was able to put a name on was Brachymyrmex cavernicola, a cute little bugger that looks more like a Paratrechina than a Brachymyrmex until you count the antennal segments. The last taxonomic revision was in 1923 (Santschi) so it is definitely due for another one. Luckily, it looks like Vinda Maharajh, a PhD student at the University of Florida, is working on one. I sent him a bunch of my samples last week and wish him luck. If you have any Brachymyrmex specimens lying around, you might consider sending them on over.

Physicists undertake stamp-collecting

2008-03-29T09:38:00.003-04:00

John S. Wilkins (Evolving Thoughts) has a nice post about physicists and taxonomy and the role of classification systems in science:

"Ernst Rutherford, the "father" of nuclear physics, once airily declared "In science there is only physics. All the rest is stamp collecting". By this he meant that the theory of physics is the only significant thing in science. Such mundane activities as taxonomy in biology were just sampling contingent examples of physics.
So it is with some amusement that I note that in order to make sense of string theory, a group of physicists have been trying to do taxonomy over string theories. Why this is more than a "gotcha!" is that since the late nineteenth century, philosophers of science have ignored classification, although some of the more important advances in physics relied on it, such as Mendeleev's Table, which drove theoretical advances in both chemistry and physics (and led even more ironically to the understanding Rutherford had of radioactivity)...."

ANTZ The RPG

2008-03-27T11:40:00.000-04:00

Unraveling the Evolutionary History of the Hyperdiverse Ant Genus Pheidole

2008-03-17T12:33:00.004-04:00

Myrmecos has a very nice review of Corrie Moreau’s Pheidole evolution paper, as well as a hilarious informal summary of the results (see image above). Read the review here and the paper here.

Some interesting links

2008-03-08T09:27:00.004-05:00

NC State University Insect Museum blog
lots of interesting stuff here. I like the idea of a blog that several people post to -- I keep trying to get my labmates to give me stuff to post about what they're doing but they're all too busy working and stuff :)

Geometry explains the benefits of division of labour in a leafcutter ant
new paper in Proceedings of the Royal Society B by Heikki Helanterä and Francis L.W. Ratnieks

The 5th edition of Linnaeus' Legacy
It's a blog carnival focusing on taxonomy and biodiversity. I'm not sure what a blog carnival is but it appears to be a roving roundup of interesting news and papers.

Darwin Live and in Concert

Ask Jane

2008-03-08T09:17:00.004-05:00

Sometimes I hear about something and I think -- gee, I should really right a blog entry about this -- and I make a little note to myself or save the link for later and then when I sit down to write the entry I think -- boy, I don't have anything interesting to say about this and I don't want to do something lame like just have a link to it so why don't I deal with this later -- and then of course I either never get to it or I just have a lame link to it. Sometimes while I'm procrastinating someone else decides to write something interesting about it. That's what happened today when Myrmecos commented on Jane: the Journal/Author Name Estimator. So go read it.

The Gigantiops Destructor Store gets a mention

2008-03-07T20:45:00.003-05:00

Looks like my cafepress store got a mention on antbase. That's cool. Makes me feel bad for not updating it in so long, though. Just remember, it's called The Gigantiops Destructor Store, not The Gigantiops Destructor Shop (cause that doesn't rhyme!).

Biodiversity Heritage Library

2008-03-04T13:06:00.002-05:00

Biodiversity Heritage Library has launched. Looks like it will be a good resource for taxonomists.

"Ten major natural history museum libraries, botanical libraries, and research institutions have joined to form the Biodiversity Heritage Library Project. The group is developing a strategy and operational plan to digitize the published literature of biodiversity held in their respective collections. This literature will be available through a global "biodiversity commons."
Participating institutions:

* American Museum of Natural History (New York, NY)
* The Field Museum (Chicago, IL)
* Harvard University Botany Libraries (Cambridge, MA)
* Harvard University, Ernst Mayr Library of the Museum of Comparative Zoology (Cambridge, MA)
* Marine Biological Laboratory / Woods Hole Oceanographic Institution (Woods Hole, MA)
* Missouri Botanical Garden (St. Louis, MO)
* Natural History Museum (London, UK)
* The New York Botanical Garden (New York, NY)
* Royal Botanic Gardens, Kew (Richmond, UK)
* Smithsonian Institution Libraries (Washington, DC)

Plazi.org

2008-02-28T15:07:00.002-05:00

Plazi.org is a new web based service that has been developed for the access and storage of taxonomic info. Myrmecos is a fan. I just gave it the quickest of look-overs, but it does look very cool. Go check it out.

Site Redesign

2008-02-28T12:51:00.002-05:00

I have recently spent way too much time redesigning my research website. Comments would be appreciated.

Awesome new scientific name: Beelzebufo

2008-02-20T09:40:00.002-05:00

So I'm sure you have heard about this new giant frog fossil found in Madagascar. It's big news. What I didn't know, and just found out last night, is that it is called Beelzebufo, which I think is an absolutely fabulous name. I really do appreciate a clever scientific name. I also appreciate all the crazy headlines this frog has inspired. I'm starting to feel bad for the poor thing:

Giant Frog Jumps Continents, May Have Eaten Baby Dinosaurs

The Whopper Hopper

Devil toad! Giant Beelzebufo bones unearthed

Found: The frog from hell

Ancient frog was as big as a bowling ball

ALL HAIL BEELZEBUFO

'Devil' frog ate dinos for breakfast

Froggie went a-killing

Prehistoric 'devil frog' was an amphibian with attitude

Devil Toad had armor, teeth

Beelzebufo - devil toad and scourge of prehistoric times

The meanest frog ever...

Meet the dinosaur toad as big as a bowling ball

A hoary, 10-pound, out-of-place frog

Happy Valentine's Day!

2008-02-14T12:54:00.003-05:00

See more great scientist valentine's at Ironic Sans

Climate change and the fate of the Amazon

2008-02-13T11:43:00.003-05:00

Philosophical Transactions of the Royal Society B has a theme issue on ‘Climate change and the fate of the Amazon.’ And it looks like it's all available online. Check it out here.

Happy belated Darwin Day

2008-02-13T11:30:00.001-05:00

Yesterday was Darwin's 199th birthday. Here is a quote that I particularly like:

Nothing before had ever made me thoroughly realise, though I had read various scientific books, that science consists in grouping facts so that general laws or conclusions may be drawn from them.
- Charles R. Darwin

Linnaeus' Legacy #4: Darwin Month Extravaganza!

2008-02-09T12:48:00.000-05:00

The Other 95% has a nice roundup of interesting blog entries in the taxonomic/Darwinian/Linnaean genres:

"the economy of nature"

species are "alloted places" in nature

"everyone's war against everyone"

These were concepts familiar to Darwin by the time he wrote On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. They influenced his thinking are solidified within his writings. Yet, these are not Darwin's own words, nor his own ideas. Other's works weighed heavily on Charles Darwin from Thomas Malthus and Gilbert White to Charles Lyell and William Paley. The words, or ideas, are none of their own as well. These words and concepts belong to Carolus Linnaeus, the namesake of this carnival and founder of taxonomy.

Linnaeus had a very ecological view on organisms and their place in nature. He was particular interested in reproduction and had a vivid imagery associated with writings when describing bisexual plants. "Nine men in the bride's chamber, with one woman" describes the 9 stamens surrounding a singular pistil on a flower. Erasmus Darwin, Charles' grandather, was similarly vivid and poetic. Darwin apparently read translations of Oeconomia Naturae and Politia Naturae in the 1840s, though I am not sure if he read the Systema, but he certainly would have been aware of it and followed Linnaeus' taxonomic guidelines. This month brings you posts in the traditions of Linnaeus and Darwin.
Deep Sea News reports on the discovery of an entirely new order of fish.
"Tube-eye is a strange fish indeed. It possesses a pair of telescopic eyes that lie anteriorly when not feeding. During feeding, the head is oriented up and back and the mouth is moved forward. The mouth cavity is balloonable and can greatly expand its size (38X). This creates negative pressure and provides suction for capturing prey."
In true linnaean fashion, the Systema Brachyurom is out!! An amazing reference for identifying every brachyuran, or true crab, IN. THE. WORLD. Can't plug this one enough! I've already downloaded it (its open access!!!) and flipped through it. It is well put together with clear photos to aid in identification. Check it out for free courtesy of the Raffles Museum in Singapore.

10,000 Birds has an interview with David Ringer, creator of Birdstack. Find about more about the bird listing website that has the "potential to become the web standard for listing". Mike also encourages bloggers who discuss natural history and ecology to register their blogs on the Nature Blogs Network.

What are the mysteries of the platypus? Oh let me count the ways... A 3lb Monkey Brain describes how the fossil record elucidates this mystery, it might not be the one your thinking of. Browse his blog for my systematic fun!

The Catalogue of Organisms reports on breaking news that will Shock and Awe™ the genetics world. Should Drosophila melangaster be maintained despite obvious paraphyly?? Or should it become the wine-cellar fly of Linnaeus? Or will the ~~evil~~ geneticists win because of their laziness to accept the rules of nomenclature?

A character analysis of moray eels is discussed over Malaria, Bedbugs, Sea Lice and Sunset. Every Monday, Rick discusses a species on moray eel on his series That's a Moray Monday. Its turning out to be a online field guide! He hints at a cool new species of Moray for the next Monday's edition so stay tuned to the blogdial.

John Lynch tells us that a new beetle is named after Roy Orbison and giant elephant shrew was recently described. Laelaps also talks about the Grey-Faced Sengi in more detail. Pondering Pikaia picks up on this amazing discovery too. While at Living the Scientific Life, a new subspecies of bird was discovered in Nepal and a giganormous rodent found in ~~New York City~~ modern day Uruguay.

Greg Laden discusses the ascent of cat breeds (with a hilarious LOLcats to boot). In thinking about the number of species of flies (not cats), The Questionable Authority has a quiz about "How many different species should these three populations be grouped in, and why?" Tune in on Monday to find out the answer!

Finally, last year Darren Naish at Tetrapod Zoology helped to blow the whistle on inappropriate activity in the field of palaeontology. Mike Taylor has the latest from Aetogate. Darren updates us on this issue and the press it has received. Christopher at the Catalogue asks what would the ICZN do about the issue? Adventures in Ethics and Science discusses the ethical ramifications of this and then explains why the "is this really that important?" attitude is detrimental, then wonders which field of science has the most integrity problems. Additional coverage is provided by The Ethical Palaeontologist, Cryptomundo, Dinochick Blogs, Laelaps, Gene Expression, The Open Source Palaeontologist, Slashdot, One Big Lab, A Blog Around the Clock, All My Faults Are Stress-Related, Dinochick again, Palaeoblog, A Three-Pound Monkey Brain, Stephen Sorrell, The Reptipage. As you can see, this is a very important issue and each blog offers their unique perspective on this and the support for ethics in taxonomy and palaeontology is overwhelming.