Nature Blog Network

Tuesday, February 26, 2008

Tuesday Toon

A Protocol for Sea Squirt Dissections

Our biology department has been having a lot problems keeping sea urchins alive here in landlocked central PA. Probably mostly from poor keeping, but they seem to be very sensitive to our wide temperature fluctuations (i.e. purple California sea urchins hate PA winters). As a back up we would like to use another organism when our urchins die off, possibly a Ciona species. Does any sea squirt biologists (Jarrett, Miriam?) have a protocol for dissecting gonad our of sea squirts? It is for a development lab. Please leave or a comment or email me (address in top right sidebar).

Monday, February 25, 2008

Lyric of the Day!

"I don't thinking drinking is a sport, but I thank you for your support"
- Shitkickers-Bartles & Jaymes

Sunday, February 24, 2008

Zen and the Art of Tidepooling

Tidepooling was an activity that made me as giddy as a kid in candy shoppe. There is little as pleasurable as exploring the minute natural saltwater aquaria and finding new creatures in each little pool. Being locked in coastline-less PA, I have not visited a tidepool in ages except when on vacation, where my last several coastal destinations have not been rocky :(

Dorid, over at the Radula, recently let me relive my tidepool giddiness by posting a primer on proper tidepooling. I'm very proud of her proper use of brittle star and sea star, as well her identification of "snail tubes" I'm not sure many non-invertebrate biologists would get that. Maybe polychaete tubes, but these tubes actually belong to a relative of the snails called Aplacophorans.

Quote of the Day!

"It is more proper to call starfish “sea stars”. Not only do they not live in the sky with stars but they aren’t fish. They are echinoderms. So from now on you can call them sea stars and avoid a lot of confusion."
- Joel from the Oceanographic Research Vessel Alguita blog

Hey guys, keep up the good work on our high seas!

Friday, February 22, 2008

Fired CNN Producer Exposes Corporate Media

Chez Pazienza, former producer for CNN, was recently fired for blogging. He finally now writes about the ordeal and exposes the corporate media facade for what it is. Its very interesting and a must read post for the day. I won't rehash him here. You should definitely go read his take on his former job and employer. But I really like this quote:

"CNN fired me, and did it without even a thought to the power that I might wield as an average person with a brain, a computer, and an audience. The mainstream media doesn't believe that new media can embarrass them, hurt them or generally hold them accountable in any way, and they've never been more wrong.

I'm suddenly in a position to do all three, and I know now that this is what I've been working toward the last few years of my career.

Awhile back I was watching a great documentary on the birth of the punk scene, it closed with former Black Flag frontman and current TV host Henry Rollins saying these words: "All it takes is one person to stand up and say 'fuck this.'"
Don't fuck with the power of the blog bitchez.


Peter sent me the coolest thing I've seen on the net in ages! The website, Dreamlines,

"is a generative drawing machine that creates a unique, ever-flowing painting after words you choose. Related images are gathered from the Net and used as raw material for the construction of your personal dream.

...The key of the piece lies in the translation between two different sets of coordinates: color and movement. The images are never actually shown. The visual output is the result of the endless drifting of a swarm of 1500 autonomous particles. The loaded images are a sort of virtual terrain for them. The direction and speed of each particle is given, at each step, by the color values of the pixel it is stepping on. The resulting path is traced to the screen, and the accumulation of them forms the dense drawing seen by the user."
Here are a few of my own drawings for "invertebrate"!

Wednesday, February 20, 2008

Is the World of Taxonomy Ready for PLoS Systematics?

Taxonomy has historically been relegated to the back alleys of the publishing world. In-house museum journals, obscure regional or specialty publications and even more obscure foreign language academy reports have hidden many species descriptions, revisions and monographs from the eyes of interested biologists. Not to say this is the only reason for current crisis in taxonomy (see Rodman & Cody 2003), but it certainly contributes. The hard work and insurmountable dedication of the taxonomist to furthering their group of interest should be rewarded and not locked away for the other 5 people in the world working on that genus of organism. Ecologists rely on species descriptions to compare the fauna they find in their studies with the published literature. The imperative nature of correct identifications of species cannot be understated in the medical, infectious disease, and parasitology literature. Without a doubt, quality taxonomic research is invaluable, in high demand and highly underappreciated by funding agencies and other scientists, even those who rely on such work (PEET not withstanding)

The lack of visibility of taxonomic research and the failure to make systematics as a whole relevant to the everyday lives of people has been a burden on the community. Much of the work is tedious yet vital to biodiversity studies, medicine and biotechnology. IrregardlessIrrespective of how one chooses to define a species, the species debate, the issue of perception is pervasive in this field. Many taxonomists are made to feel inferior to their colleagues doing experimental work who bring in much larger grants. The truth of the matter is that taxonomy is not a profitable venture for academic institutions why rely in part on the money they skim off of grants. It is a traditionally an inexpensive field, even with the use of molecular tools to aid in phylogenetic reconstructions. You can easily get by with a microscope, computer and digital camera. DNA extractions are relatively inexpensive and you can send the DNA product off to get analyzed elsewhere affordably, not needing to purchase expensive sequencing equipment.

Taxonomists need to improve the visibility and relevance of the field to ensure a continued, or at the least renewed, interest for the study of species, either from a theoretical, philosophical or practical framework. One way to contribute to increasing the visibility of taxonomic research is to publish in Open Access (OA). Several studies have shown there to be a citation advantage in OA papers (Eysenbach 2006). Zootaxa has taken the initiative in the taxonomy world by offering to publish any peer-reviewed taxonomic work free of charge for subscriber access and $20/page for OA. Other taxonomic "niche" journals exist with various financial differences, but have yet to attain the reputation of Zootaxa to my knowledge. But it is my own feeling that Zootaxa is only known well among other taxonomists, with the majority of other beneficiaries either unable to obtain articles because the bulk of the articles are locked behind the subscriber wall. This also has the effect of making less text available for search engines, such as Google Scholar.

The Public Library of Science (PLoS) may help to alleviate part of the problems of visibility. They have grown to represent the standard in OA publishing and have a successful business model. Their success among scientists can measured by the fact that between all their publications they are PLoS ONE alone is publishing on average 50 high quality papers per week. This is higher than journal, even the weekly big names. It is clear that their model is successful and scientists are actively seeking them out to publish their research. This is a clear argument in favor of wide dissemination (Chapter 3, Recommendation 8A of the Code):
"Authors have a responsibility to ensure that new scientific names, nomenclatural acts, and information likely to affect nomenclature are made widely known. This responsibility is most easily discharged by publication in appropriate scientific journals or well-known monographic series and by ensuring that new names proposed by them are entered into the Zoological Record."
PLoS can make nomenclatural acts widely disseminated by providing them free of charge and out in open for all interested individuals with computer access. The steadily increasing popularity of PLoS ensures taxonomic work reaches a wide audience with a broad range of backgrounds. For instance, if you are working on parasites in humans and are describing a new species of muscle tissue boring pathogenic nematode you can tag the article as "medicine", "Nematoda", "New species", "Systematics", "Pathogen", etc. to reach audiences in non-parasitology fields.

Why would a taxonomist want to reach non-taxonomic areas of science? Citations are low in taxonomy. Species descriptions are read, the names are used in many publications, hopefully with author and year, but somehow the paper describing said species remains out of the list of references. This means indexing services like PubMed and Web of Science miss the uncited species descriptions in the tangled web of cross-reference. For example, Drosophila melanogaster Meigen, 1830, should be the most cited paper in recorded history due to the amount of work on this model organism. So what of biodiversity studies with hundreds of species? This does pose a problem. Nowadays, there is supplementary online material and the citations could be referred there so long as they are properly indexed and the gods who fiddle around with such productivity metrics recognize these citations.

Another argument to get your work widely read is that universities aren't appearing to hire people to do basic taxonomy anymore. They need another hook, perhaps molecular evolution or ecology. Even museums are tending to hire individuals with outside specialties. I'm not sure where the future of taxonomy may lie, but larger questions need to be addressed than just what is out there. Taxonomic research helps in many areas of biological science. The more people that know of your work, the more opportunities may be to collaborate on new projects with different directions, making you a more viable applicant. Besides who wants to invest so much into something only to see it hidden away forever?

Are there any barriers to publishing a species description with PLoS? Yes, Chapter 3 of the Code, Article 8.6 states:
"Works produced after 1999 by a method that does not employ printing on paper. For a work produced after 1999 by a method other than printing on paper to be accepted as published within the meaning of the Code, it must contain a statement that copies (in the form in which it is published) have been deposited in at least 5 major publicly accessible libraries which are identified by name in the work itself."
So species names published in an electronic format are only valid if depositions of the article in question are made at a minimum 5 public institutions. These can be public, university and museum libraries. This barrier is easily overcome if PLoS makes it easy on the authors by forging an agreement 5 institutions to deposit papers in their collections. I would recommend the Smithsonian, the Field Museum and any 3 universities in the U.S. The authors can even archive a paper in their own university's or museum's libraries. Conveniently, PLoS does offer itself in print version for those interested in deforestation.

Another barrier is the high cost of OA publishing. Currently, PLoS ONE charges $1250 for a research article, though they do offer fee waivers to authors who cannot the steep price. For the average working taxonomist, the price would need to drop to at most $600. This is a price I was quoted for a small american journal for a 20 something page description of a new shrimp with COI phylogeny. It was actually twice that, but I can some page charges waived for being a society member. My coauthor and I were shocked when we received the estimate. For almost the same price I could have published OA somewhere else. The costs are especially prohibitive to taxonomists from the developing world. Many of them have done a superb job and picked up the slack after north american taxonomy slipped away because of poor funding. Yet their funds are even less than ours in most cases.

In conclusion, OA publishing offers taxonomists higher visibility, potentially higher citations and a broader readership. The barriers to electronic publishing can be easily overcome with a little initial work. PLoS is the leader in OA publishing and has a strong reputation to maintain among the non-OA or hybrid journals that exist out there, thus the quality of research coming from PLoS journals is high. In particular PLoS ONE, offers several features attractive to taxonomists and idealistic scientists like myself. Their system allows any user to annotate, comment and respond to articles becoming a part of the permanent record of that article. This post-review system allows articles to become a conversation. If another taxonomist were to discover a new character 10 years after the publication of a species name, they could go that article and make an annotation or comment on that article that could then be considered by all other readers. Taxonomists have little to lose and everything to gain by publishing with PLoS and choosing OA.

Eysenbach, G. (2006) Citation Advantage of Open Access Articles. PLoS Biology, 4, e157.

Meigen, J.W. (1830) Systematische Beschreibung der bekannten europäischen zweiflügeligenInsekten, Bd. 6. F.W. Forstmann, Aachen.

Rodman, J. E., and J. H. Cody (2003) The taxonomic impediment overcome: NSF’s Partnerships for Enhancing Expertise in Taxonomy (PEET) as a model. Syst. Biol. 52:428–435.

Tuesday Toon (Belated)

From Gary Larson's Bride of the Farside.

The Beagle Project: Making Scientists Sexy

You wanna look this good? You wanna be this hip? Go without delay to The Beagle Project Store and shop till you drop! Not only will look as sexy and hot as myself (also sporting a Dogfish Head Raison de' Etre), but you will be supporting the most noble natural history and education project evah!

Book Review: Microcosmos

Microcosmos: Discovering the World Through Microscopic Images from 20 X to Over 22 Million X Magnification. This postcard sized book is a collection of unbelievable microscopic photography from the archives of The Science Photo Library assembled by Brandon Broll. I was in awe of the visuals and excruciating detail of the images. Below is an example page from the amazon webpage.

The book is organized into 6 sections: Micro-Organisms, Botany, The Human Body, Zoology, Minerals and Technology. Each section takes you through a visually stunning micro-world. There are 205 full page Scanning Electron Microscope (SEM) images and the magnification and description accompanies each of the images. Every image has a unique feature that will leave the reader searching for more answers.

A great coffee table addition or a thumb-through for inspiration, Microcosmos will undoubtedly leave you in amazement at the little world that surrounds us. At less than $20 on amazon I highly recommend this for your library (looks great next to Reef)!

One of my favorite images from the book, scanned in by myself.

Self-Promotion Yay!

Bora has an extensive interview with me up at A Blog Around the Clock. It's all about me! Yay!

Work with an Invert! - Mollusc Minigrant

I am glad to remind you that the deadline for the Conchologists of America Academic Grants 2008 cycle, February 28, 2008, is fast approaching.

Grants in amounts up to $1,500 will be available to qualified persons undertaking field or laboratory research on Recent or fossil mollusks. The committee consists of Dr. Henry Chaney (Santa Barbara Museum of Natural History), Dr. Gary Rosenberg (Academy of Natural Sciences of Philadelphia), and José Leal (The Bailey-Matthews Shell Museum).

Please check the COA site at for more information, application instructions, and other requirements.

The site also provides a list of funded research projects at

Tuesday, February 19, 2008

Lyric of the Day

"Another Joker in the White House, said a change was comin' round
But I'm still workin' at The Wal Mart and Mary Alice, in the ground
And all them politicians, they all lyin' sacks of shit
They say better days upon us but I'm sucking left hind tit
And the preacher on the TV says it ain't too late for me
But I bet he drives a Cadillac and I'm broke with some hungry mouths to feed

I wish I'z still an outlaw, was a better way of life
I could clothe and feed my family still have time to love my pretty wife
And if you say I'm being punished. Ain't he got better things to do?
Turnin' mountains into oceans Puttin' people on the moon"
- Puttin' People on the Moon by Drive By Truckers from the album The Dirty South

Happy Belated Presidents Day!

Bioturbation: An Update on Darwin's Last Idea

Just got wind of a conference that sounds pretty awesome: Bioturbation: an update on Darwin's last idea. This is of course in reference to one Darwin's last great works: The formation of vegetable mould through the action of worms, with observations on their habits. The conference objectives are:

(1) To bring together scientists from different disciplines to provide an update on bioturbation from different perspectives, such as ecology, geochemistry, marine biology, paleontology, etc.

(2) To stimulate the exchange of ideas across the marine/terrestrial and paleo/present boundaries. We strongly invite “crossing-boundary” presentations.

(3) To present the state-of-the-art in theoretical concepts, mathematical models, experimental data acquisition techniques, and existing datasets.

We stimulate "off the record" presentation of previously unpublished scientific results, and we will allocate ample time for formal and informal discussion among the attendees.

Organizing committee: Bob Aller (SOMAS, SUNY Stony Brook), Erik Kristensen (Institute of Biology, Univ. Southern Denmark, Odense), Franck Gilbert (EcoLab, Univ. Toulouse), Jack Middelburg (Dept. Ecosystem Studies , NIOO-KNAW, Yerseke), Filip Meysman (Lab. Analytical and Environmental Chemistry, Free University of Brussels).

Work with an Invert! - Curator of Coleoptera

P O S I T I O N (CURATOR): E n t o m o l o g y – C o l e o p t e r a

At the "Zoologische Staatssammlung Muenchen" (ZSM) - a research institute in Zoological Systematics (see <>) - a free position (direct for three years, option for permanent position) for a zoologist/coleopterologist is offered starting with 1st July 2008.

Functions: Head of the section "Coleoptera" (see <>) with about 4 million specimens of world-wide importance. Scientific research on Coleoptera
including taxonomy, phylogeny, faunistics, or biogeography based on grant money. Increase,
documentation, and curation of the collection. We also expect information and reference for
guests and corresponding asks, also assistance in administration and public relations of the ZSM.

Requirements: PhD-degree or equivalent in Zoology and detailed knowledge in systematic
entomology, particularly taxonomy of Coleoptera, are required. Perfect knowledge of German
language is necessary. Applicants with personal experience in modern systematic methodologies (e.g., molecular methods, data-bases, SEM, morphometry) will be preferred. Expert knowledge and experience in curating scientific collections is welcome. We also
expect activities concerning public relations of the museum and with respect to associated

According to personal conditions and juristic requirements the contract will be for three years as "Entgeldgruppe 13 TV-L" with an option for a permanent position as "BesGr A 13", if overall
performance is adequate and juristic requirements are fulfilled. Handicapped applicants will be
preferred in cases of equal qualification. We want to increase the percentage of women in
science at the ZSM. The position can also be divided into two half-time ones.

Send your application with curriculum, list of publications and reprints (copies or CD-ROM with pdf-files) of the five most important publications to:

The Director,
Zoologische Staatssammlung Muenchen,
Muenchhausenstrasse 21,
D-81247 Muenchen, Germany

U N T I L MA R C H 31st 2008

Work with an Invert! - Butterfly Evolution and Bioinformatics

Post-doctoral Research Associate in Molecular Evolutionary biology/Bioinformatics

We seek a post-doctoral researcher with training/experience in bioinformatics and large-scale sequencing to conduct research in two projects based on 454-sequencing and related to population dynamics and molecular evolution. The post doc will work in a large international research group.

One project is concerned with a highly variable gene (Pgi) with strong association with individual performance and fitness in the Glanville fritillary butterfly, which has been the focus of large-scale research since 1991. The research involves sequencing and analysis of large population samples. The second project is concerned with the identification and quantitative measurement of the abundances of fungal species in decomposing tree trunks. This project is related to an ERC-funded project on metacommunity dynamics of polyporous fungi. In both projects the sequencing will be carried out at the nearby high-throughput laboratory of the Institute of biotechnology, University of Helsinki using massive parallel sequencing methods.

PhD and prior experience with bioinformatics and molecular biology methods is required. Strong candidates would additionally have interest in molecular evolution and/or population genetics. The position is available for two years with possible extension for up to two more years.

We offer a highly international research environment with excellent possibilities to interact with researchers in ecology and evolutionary biology, molecular biology, mathematics and statistics. Salary and social benefits according to the University of Helsinki Salary Scale, around 3,100 €/month (negotiable based on experience).

Applications including a short CV (max 3 pages), list of publications, and the e-mail addresses of two researchers willing to write a letter of reference should be sent to ilkka.hanski[at]helsinki[dot]fi (cc tuuli.ojala[at]helsinki[dot]fi; write "mol ecol post doc position" on the subject line). For more details on the research group see Consideration of applications will begin immediately and continues until the position is filled.

Lobster Biology Course

Go to the Gulf of Maine and learn about lobster this summer!

"I am very excited to tell you about the Biology of the Lobster course which will be offered at the Shoals Marine Laboratory on Appledore Island, Maine, from July 7 to July 14, 2008. Please help me bring this to the attention of those who might be interested. The course is particularly well suited for upper-level undergrads, beginning graduate students who work with lobsters or related animals, marine educators, and conservationists and managers.

This new course brings together several lobster biologists (Jan Factor, Stan Cobb, Rick Wahle, Win Watson, and 3rd generation Isles-of-Shoals lobsterman Ed Foye) for what promises to be an exciting first-hand study of lobsters in the Gulf of Maine.
For additional information visit

Monday, February 18, 2008

Quote of the Day!

"But they’re the most hypocritical judge of people we have in this country. And it bugs the hell out of me. They act like their Christians. And they’re not forgiving at all."
-NBA star Charles Barkley on "fake christians" in interview with Wolf Blitzer. Awesome. He supports gay marriage and is pro-choice. (Click link for the video). Hat tip to Bora.

Todays Keywords

I always enjoy discovering how people discover my blog. For the porn purveyors from Malaysia, U.K. and elsewhere, I apologize if it is not the species you were looking for. Invertebrate porn can be just as interesting, if not more, to watch. I very glad people are coming across my extensive Cheatognath phylogeny posts (here, here, and here, and the blog of one a Chaetognath lover)! Who the heck is this Jason Robertshaw guy anyways and why is he on my blog???

Previous rant on keywords can be found here.

Sunday, February 17, 2008

Heavy Snow = Light Blogging

We got absolutely dumped on a few days ago. Finally winter is here!! So I am doing what any snow-loving midwesterner would do. Cross-country skiing! For those of you snowed in, get out and have some fun. I'll post later when I'm thawing out.

Trying out the gear after its been in storage for a year. Just needs a little wax!

Thursday, February 14, 2008

CNN Producer Fired for Blogging

CNN producer Chez Panzienza was fired from CNN for blogging. Keep posted to his blog for more details. He promises to get a post up about it in the next day.

"Chez Pazienza, a producer at CNN assigned to American Morning, was unceremoniously fired from his job today — without severance — over the content of his popular and edgy blog, Deus Ex Malcontent (warning: adult language). He had worked for CNN for four years, beginning as a Senior Producer in Atlanta.[...]

According to Chez, he was terminated for violating network policy by not running what he was writing through their vetting system. So he was fired not for blogging but for the content of his blog. “It’s not that I’ve been writing,” he wrote in an email. “It’s WHAT I’ve been writing.” That may be the official decision, but the truth is he was fired because he had the balls to write about the industry without telling CNN. I would add that there is no mention of his connection to the network on his site, and as a producer, it’s hard to justify the notion that he’s in any way a public figure or publicly connected with the company." (from Terry Heaton's PoMo Blog)

Hat Tip to Further Thoughts.

Quote of the Day

" There is nothing wrong with sexual fantasy and spanking your monkey, but how about instead of buying prepackaged corporate fantasy that harms both women and men, you use your fucking imagination?"
- The venerable Physioprof on Sports Illustrated new website devoted to their swimsuit issue.

Wednesday, February 13, 2008

Work with an Invert! - Lobster Field Technician

The AVC Lobster Science Centre invites applications from qualified individuals for the technical support position of LEAD FIELD TECHNICIAN on a full-time basis. The individual will provide technical support in the field service unit & laboratory research programs in the AVCLSC. Please feel free to distribute this posting to those you see fit.

More information can be found at:

Quote of the Day

"Step 1. Realizing and embracing the enjoyment of nature.

This is the critical first step in the process. If one does not like nature, there is definitely no future for that person in taxonomy. Most who fail at this Step ultimately become accountants." 

- Neil Evenhuis (2007) Helping solve the "other" taxonomic impediment: completing the eight steps to total enlightenment and taxonomic nirvana. Zootaxa, 1407, 3-12. Open Access!

Tuesday, February 12, 2008

Earthworms as HazMat Workers?

Its a little old news, but I was clearing out old bookmarks in my browser and thought this was too cool to not post on. You can read the whole story here.

Did You Know?

The internet is taking over. Better get with the program and get left in the dirt. For more information, or to join the conversation, please visit -- Content by Karl Fisch and Scott McLeod, design and development by XPLANE.

Monday, February 11, 2008

WTF Zootaxa!

How are you going to be the "world's top journal of biodiversity discovery" if you present this news on your frontpage? Can you spot the error? Leave a comment!

Sunday, February 10, 2008

Advances in Crustacean Phylogenetics

I was a little slow on this one, but the 1st annual symposium on Advances in Crustacean Phylogenetics will be held October 10-12 in Rostok, Germany.

We are pleased to announce an international symposium to explore recent advances in crustacean phylogenetics based on morphological and molecular data. The idea is to bring experts from different fields together to discuss

(1) the place of crustaceans within arthropods,
(2) the phylogeny of single sub-taxa and
(3) the contribution of certain character complexes to the phylogeny of Crustacea.

Submission of poster abstracts is in July, 2008. This promises to be a historical meeting. I so wish I could attend but have no funds...

Dragon Dew

A reader forwarded me this amazing image by photographer Martin Amm. Feel free to leave critiques over at his webpage for this image and peruse his other awesome photos (especially the macros).

Saturday, February 9, 2008


New additions to the Spineless Wonders blogroll:

Myrmecos - Insects, especially ants, and amazing photography with a healthy mix of extracurricular posts. I've been following Alex Wild's blog for months, don't know why I haven't blogrolled it yet!

The Ant Room - A graduate student at Boston University studying the ant fauna of Tiputini Biodiversity Station in Ecuador an blogging about it.

Introducing the Ecology and Systematics Blogroll!

10,000 Birds - Natural history of birdies.

Barcode of Life - I'm not advocating barcording, but I think their blog is interesting and useful as a tool and not as a sole method for describing new species.

Behavioral Ecology Blog - Its not his fault Michigan's football team sucks, at least he can write awesome posts on all things ecological!

Biodivcontext - One of several blogs by ant taxonomist and science consultant Donat Agosti from Switzerland.

Evolving Thoughts - Australian philospher of science John Wilkins blog. Excellent, well thought out posts on matters philosophical of species, biodiversity and occasional rants.

iPhylo - Blog of Rod Page in the U.K. exploring systematics and offering practical tools for working with phylogenies.

Linnaeus' Legacy - Blog carnival for matters taxonomical.

Oekologie - Homepage for the blog carnival of ecology.

Systematics and Biogeography - "The Companion Blog for topics addressed in the book Foundations of Systematics and Biogeography."

Voltage Gate - Blog of writer and journalist Jeremy Bruno who highlights issues and research concerning ecology, evolution and conservation.

Thursday, February 7, 2008

Linnaeus' Legacy #4: Darwin Month Extravaganza!

"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.

Wednesday, February 6, 2008

New Malacology Open Access Journal

For everything malacological and freely available over the net! But they make no mention of page charges...

"MalaCo (ISSN 1778-3941), a peer reviewed journal referenced by the Zoological Record, is an electronical open access publication. Articles, in French or English, focus on ecology, biology, systematics and conservation of continental Molluscs. MalaCo publishes original work as well as news, short notes and practical tools for species identification.

Since November 2007, articles are available on the MalaCo website as soon as they are accepted. To submit papers, please see author recommendations and contact the editorial team.

Hoping to publish your work soon,

Best wishes,
The editorial team

Jean-Michel Bichain / MNHN Paris / France
Xavier Cucherat / Biotope consultancy / France
Benoît Fontaine / MNHN Paris / France
Olivier Gargominy / MNHN Paris / France
Vincent Prié / Biotope consultancy / France

Journal Home:
Diffusion: open access
Online ISSN: 1778-3941
Frequency: annual or biennial
Language: French and English
First issue: May 2005
Current issue: 5 / 2007
Referenced by: Zoological Record - CIRS - BiologyBrowser (Thomson)

Contact: jean-michel[dot]bichain[at]educagri[dot]fr"

Tuesday, February 5, 2008

Carnival of the Blue #9: Make 2008 a Blue Year!

2008 is the year to LIVBLUE: "Live like you love the ocean." That is why are ocean bloggers. The ocean holds a special place in all of our souls. A place where life came about, evolved and was cradled. A historical refuge from extinction. A place where bountiful resources nurtured early civilizations. A superhighway and living market for modern civilizations. Yet a place where we can rest our weary bodies, contemplate and find inspiration.

But the ocean is heaving and sighing with the weight we have put on its back. Its bounty is growing scarcer, its resources diminishing. Once a refuge, now plastic and debris, oil spills, toxic chemicals and metals, munitions dumping, and other ailments have made the watery milieu an obstacle course for its inhabitants and there are no do-overs in this game. This may not be news to most of us. As ocean bloggers, we become accustomed to catastrophe, often the harbinger of bad news.

There is another route we can take. We can become messengers for sustainability, accountability and reformation. Humans have a close connection to the water. We are evolved from it. We are born into it. We bath in it, letting it embrace us as we cleanse ourselves. We drink it and made up of it. Not all humans will share in the full enthusiasm and passion of an ocean blogger, but they are interested in the ocean, even if never having been there. They eat from its cornucopia. They buy products that were shipped across the seas on ocean liners. They feel a pain and sense of loss when shown oil-covered seagulls and otters, or sea turtles and sharks wrapped up in thin fishing wire. I have faith in people that they generally want to do whats right.

I am calling upon all ocean bloggers to use the power of the proverbial pen in 2008 to dedicate their writing not to solving these issues. Politicians and policy-makers do read us. Everyday people read us. Our pen is better suited to educating people on not what the problems, but why they exist, who is responsible, what can be done at a local level and how to sustain a lasting commitment to the health and sustainability of our oceans and its resources.

A few weeks ago I organized and gave a session on Real Time Blogging in the Marine Sciences at the North Carolina Science Blogging Conference with my ocean blogging colleagues Peter Etnoyer from Deep Sea News, Jason Robertshaw from Cephalopodcast, Rick MacPherson from Malaria, Bedbugs, Sea Lice and Sunsets and Karen James from The Beagle Project. It was a learnign experience for myself and I think its safe to say for everyone involved, be it the co-moderators and the audience.

Real time blogging to me is the art of bringing the excitement of discovery and the process of being a discoverer to the front door of the average citizen. It captures the immediacy of the moment in all of its unedited glory. There was a lot discussion generated, which would have gone on if it weren't for the 70 minute time limit. Rick has a great analysis of our session, so I won't belabor the point here. Jason video-taped the session and has it archived here for your viewing pleasure. Additional coverage includes photos from myself (here and here too), swag from Rick, commentary and analysis from Peter and Karen as well. I came away from the whole conference with a renewed interest in blogging as a tool for public discourse and now feel more determined than ever to blog, one of several reasons I have joined the crew at Deep Sea News.

But this Carnival of the Blue is not about me, its about ocean blogging. I feel, in the water, that 2008 is going to be a big year for the Blue. It is the International Year of the Reef. Conversation has already been going on reef conservation in anticipation of this event. In 2008, I expect ocean blogging to increase, more bloggers, more discussion, more solutions. Last month, Mr. Byrnes gave us an excellent entry into this year with Carnival of the Blue #8. The Carnival of the Blue, started by Mark Powell at Blogfish, is showing steady growth. I hope it continues and that there will be more submissions from new ocean blogs and other blogs that are talking about ocean related issues. This month we have a mix of both.

Before you continue reading, head over to Cephalopodcast and start playing the latest internet radio program offered by Jason Robertshaw. Among the many pearls of marine news Jason finds, this episode also features an interview Mark Powell where they discuss the Carnival of the Blue and ocean blogging. His soothing radio voice will make a wonderful narrative while you peruse this carnivals offering.

Corey at 10,000 Birds tells us of his discoveries of the maritime avifauna on the Santa Cruz island, part of the California's Channel Islands. In particular the Island Scrub Jay, a close relative of my favorite bird from my Monterey days, the Western Scrub Jay. Special bonus: a pod of dolphins on the boatride!

A common theme ocean is that of "shifting baselines". A term coined by marine biologist Jeremy Jackson to refer to the idea that each generation has different view of what the baseline is because they only remember what the world was like when they were growing up. Jennifer Jacquet at the Shifting Baselines blog illustrates this point well with a discussion of baselines shifting as evidenced through ship captain's logbooks. Sheril Kirshenbaum at The Insection tells us that the next hot fishery is Hagfish. Which makes me wonder, will fish sticks soon be fried hagfish slimeballs? As Jennifer would say, "... just another shifting baseline..."

Public perception is important to individuals and corporations. Some ways of perceived can be clever while other irritating at best. Rick at Malaria, Bedbugs, Sea Lice and Sunsets explains the history behind the mermaid in the Starbucks logo and discusses what is the marine world equivalent of the cute and cuddly mascot, Woodsy Owl. Additionally, Miriam at The Oysters Garter wonders why Oceana is trying to spread its conservation message by spam.

Photo from The Saipan SCUBA Diving Blog

Rick McPherson again offers us brief natural history of the Crown of Thorns sea star. The ending is not a happy one for Indonesia's corals. But thankfully for the Marianas, The Saipan SCUBA Diving Blog tells us that the humphead wrasse is one the few predators for the toxic Crown of Thorns. Unless, of course, its hunted away. An excellent lesson on the natural history of this fish, Saipain SCUBA brings it home with an intense discussion of the conservation of large reef fish, politics, spearfishing, tourism and the economy. This is the editor's choice for this month's Carnival of the Blue.

Emmett Duffy at The Natural Patriot offers us beautifully narrated journal entry from his latest research excursion to Jamaica where he was "filled with a powerful sense of calm and gratitude and harmony". So touched was he by his jamaican experience he named this new species of social shrimp Synalpheus irie, irie being rastafarian for "high emotions and peaceful vibrations".

Last month, sushi was on several bloggers minds. Deep Sea News (starting with this), Blogfish, and Shifting Baselines (starting with this) weigh in. Kate Wing at the NRDC switchboard would like to point out that tuna don't even get respect on broadway!

Finally, Mark H at the Daily Kos, in his marine life series, shows us the anatomy of the gastropod shell laden with pictorial examples.

Addendum: In my late night haze I forgot to plug the Systema Brachyurorum. The Raffles Museum blog has made this comprehensive publication available to the public to encourage a concrete taxonomy, use of names and guide to identification oof brachyuran crabs.
"This 286-page work contains 6,793 valid species and subspecies, 1,271 genera and subgenera, 93 families and 38 superfamilies, making it the most comprehensive to date. And with references as recent as January 2008, it is also the most up-to-date."
That is it for this edition of the Carnival of the Blue, Kate Wing will be hosting #10 in March. Remember to live like you love the ocean.

Electoral Compass Confirms I'm Pretty Darn Liberal

As if I didn't know that. I'm just barely touching Obama. I thought I was an Edwards guy, but was Obama the whole time. Who Knew! Go to Electoral Compass to see where you lie in political landscape.

Penn State Postdoc in Agroecology

Post-doctoral Scientist in Agroecology
Penn State University
Depts. of Crop and Soil Sciences and Entomology
Interdisciplinary study on weed population management and dynamics, arthropod community, soil quality indicators, nutrient cycling and agronomic properties in organic cropping systems. The successful candidate will serve as project manager, analyze weed, arthropod, soil C and N, agronomic, environmental and economic data; collaborate with other investigators on project to publish findings, and participate in extension and grant-writing activities. PhD in weed-, arthropod-, soil- or agro-ecology required. Experience working with complex systems studies is desired but not required. The post-doctoral scientist will work directly in collaboration with David Mortensen (weed ecology), Mary Barbercheck (arthropod ecology), and Jason Kaye (biogeochemistry), graduate and undergraduate students, technicians, and a farmer advisory panel in guiding the research and outreach education associated with the project. Please send CV and list of 3 references to Mary Barbercheck, meb34[at]psu[dot]edu, by February 29, 2008. For further information, contact Dave Mortensen, Penn State Dept. of Crop and Soil Sciences, dmortensen[at]psu[dot]edu

Monday, February 4, 2008

Oops! Another Discovery Institute Abuse & Misuse

I guess its to be expected, Intelligent Design proponents just can't seem to tell the truth. Case in point: Casey Luskin, a Discovery Institute lackey attempts his first take at participating in the Bloggers for Peer-Reviewed Research Reporting (BPR3) with a post demonstrating how a recently published article in PLoS ONE using the icon copyrighted by BPR3. Anyone is free to use this icon, you've seen it many times on this blog, so long as they register their blog and abide by the guidelines of this organization. The icon is important not only because it signifies that a post is a thoughtful commentary on a peer-reviewed research article that goes beyond the press releases, but because it contains code that aggregates your post onto an RSS feed with all the posts using the icon and centralizes commentary on peer-reviewed research reporting. I include the icon in post as I will discuss the article simultaneously with a discussion of this issue of fraud.

Luskin failed to register his blog and merely copied and pasted the icon image without any code. Though this is a copyright violation, it also violates a couple of the guidelines.

4. The post author should have read and understood the entire work cited.
This is of course arguable but reading the conclusions Luskin draws from his perverted view of the article in question (open access download here), it may be indeed be argued he didn't understand the "entire work cited". But thats not enough. Anyone is allowed to use the icon and aggregation service in so far as the user abides by the rules and the work is peer-reviewed. What two scientists really have the same interpretation of an experiment?
5. The blog post should report accurately and thoughtfully on the research it presents.
As Mike at The Questionable Authority succinctly states in his analysis of the issue:
"The hard part is ensuring that the posts more or less fulfill the "accurate and thoughtful" part of that equation. That's handled as a community effort."
Luskin's commentary is not accurate. I'll leave the "thoughtful" open to your interpretation.
Editor's Note: Here is where I'll discuss a few items of the paper in reference to Luskin's post and what Orgel's article stated. I believe this follows the guidelines of BPR3 while counteracting erroneous claims of another blogger.

ResearchBlogging.orgThe article in question is an essay by the late Leslie Orgel of the Salk Institute that discusses the challenges facing the formation of metabolic cycles on prebiotic earth. It is a well-written and thoughtful essay that explains the difficulties with the evolution of the reverse citric acid cycle, hypothesized to operate under a prebiotic chemical environment. Luskin attempts to frame Orgel's essay under an irreducible complexity filter. He claims that Orgel
"... essentially assumes that cyclic metabolic pathways are irreducibly complex systems that require a large number of parts in order to function—including many side pathways that can remove products that will disrupt the cycle. In Orgel's view, it is not plausible to contend that such complex systems, with all of their numerous required components, would simultaneously come into existence."
Orgel in fact didn't make any assumptions about irreducible complexity. Luskin is putting words into his mouth. Orgel lays out a road map for making progress with the origins of life question:
"What is essential, therefore, is a reasonably detailed description, hopefully supported by experimental evidence, of how an evolvable family of cycles might operate. The scheme should not make unreasonable demands on the efficiency and specificity of the various external and internally generated catalysts that are supposed to be involved. Without such a description, acceptance of the possibility of complex nonenzymatic cyclic organizations that are capable of evolution can only be based on faith, a notoriously dangerous route to scientific progress." (emphasis added)
Orgel's problem is with the lack of experimental evidence to support some of the theory. He does not hint at the possibility of giving up on the questions, throwing his arms up and shouting "It was an intelligent designer!" Quite the contrary, he wants more work to be done and encourages further investigation into the evolvability of cyclic metabolic pathways. In the section of the essay called "Peptide Cycles" he states:
"More complex proposals along these lines need to be supported by experimental evidence or compelling theoretical arguments based on the known properties of amino acids and peptides. Claims that they exist cannot be taken seriously without support from experimental or theoretical chemistry."
To me, this statement sounds very anti-ID, since ID and the concept of irreducible complexity asserts that in the end all we have are claims and faith and no hard statistical evidence. One of his concluding sentences really hits home the authors dedication to promoting hard, evidential science:
"Theories of the origin of life based on metabolic cycles cannot be justified by the inadequacy of competing theories: they must stand on their own."
More breakdown at The Questionable Authority and go to's blog to weigh in and join the discussion with the 20+ commenters there! Law Evolution Science and Junk Science weighs in.

Orgel, L.E. (2008). The Implausibility of Metabolic Cycles on the Prebiotic Earth. PLoS Biology, 6(1), e18. DOI: 10.1371/journal.pbio.0060018

A Day of Mourning for Ernst Mayr

via Darwin's Bulldog...

Today marks the 3rd anniversary of Ernst Mayr death. He will always go down as one of the greats. Click over to Dispersal of Darwin for more (the link above).

Sunday, February 3, 2008

Quote of the Day

LOL Bug Girl, I love this quote from her post I am a Gender Traitor.

"Well, gosh, I guess I’m a traitor too for not voting the vagina party line, and looking at the candidates’ actual platforms. To take this to the extreme, would the NOW group support Ann Coulter as a candidate just because she has a uterus?"

OK, now go read the rest of the post and her wonderful blog. Don't forget to add her to your RSS!

Saturday, February 2, 2008

Carnival Time!

I'm hosting Carnival of the Blue, an ocean themed carnival, on Tuesday Feb 5. I'm also hosting Linaeus' Legacy also, a taxonomy themed carnival, on Friday Feb 8.

So get those submissions to me asap for either or both carnivals! Just leave a link in the comment thread or email me at kzelnio::at::gmail::dot::com.