Nature Blog Network

Sunday, December 30, 2007

Quote of the Day

"The discrepancy between the histories of populations and the histories of genes within those populations is the biggest problem afflicting the phylogenetics species concepts."
- Coyne, J. A., & H. A. Orr. 2004, Speciation. Sunderland, Sinauer Associates, Inc.

Saturday, December 29, 2007

Hey English Majors!

How do you cite a translation of a text? Do I include the original author followed by the translators, all as authors, and the year of the translation?

For instance what I want to cite is Hennig (1966). But I have and use a translation (from German) of his text. So do I ignore the translators and go with the traditional

Hennig, W. (1966). Phylogenetic Systematics. University of Illinois Press, Urbana. (i've seen this is an article)


Hennig, W., D.D. Davis, R. Zangerl (1999). Phylogenetic Systematics. University of Illinois Press, Urbana.

Quote of the Day

"Nor shall I here discuss the various definitions which have been given of the term species. No one definition has as yet satisfied all naturalists; yet every naturalist knows vaguely what he means when he speaks of a species."
- Charles Darwin (1859) On the Origin of Species by Means of Natural Selection, Murray

Long-Lived Lobster NPR Podcast

NPR's Krulwich on Science has a podcast on the long lives of lobsters. Its pretty entertaining with a Gilbert & Sullivan song even! It seem like they never age and never die from within (i.e. old age). Or perhaps it is all the Guinness? Interesting research out of Boston University's Marine Program.

Friday, December 28, 2007

Spineless Wonders of the Web Blogrolling

I've updated my Spineless Wonders of the Web Blogroll finally. I keep adding RSS feeds to my Google Reader without entering them into my blogroll. The following websites have an invertebrate focus or at least theme. I highly enjoy each one and you should too!

A Snail's Eye View - natural history and gastropods
Biodiversidad Venezuelica (in spanish and english) - marine invertebrates of Venezuela
Biological Tales from the Brine Queen - marine invertebrates
Bug Girl - insects
Catalogue of Organisms - arachnids, other terrestrial invertebrates, flora and fauna
Cephalopod Centerfold - cephalopods!
Cephalopodcast - cephalopods and marine education
Circus of the Spineless - monthly traveling circus devoted to inverts
From Archaea to Zeaxanthol - marine inverts and the Red Sox
Gossamer Tapestry - Lepidopterans and insect diversity
I'm a Chordata, Urochordata! - sea squirts and marine ecology
iSpiders - spiders and phylogenetics
Microecos - all creatures great and small...
Natural patriot - crustacean biologist, ecologist, environmental defender
Ontogeny - ants and other insects
Ron's Montana Musings - invertebrate biologist, aquarist
Snail's Tails - snails, isopods, rotifers and delicious food!
Squid - need i say more?
The Digital Cuttlefish - the world in verse
The Missing Cluster (in french) - invertebrate phylogenomics
The Oyster's Garter - musings of a science writer and marine invert enthusiast
The Radula - nudie lover

Quote of the Day

"You do not know what you are doing in any area of biology that involves any comparative work if you do not have a clear idea of what comprises a species, and how different species relate to one another."
- Ferris VR (1999) Species concepts do matter in nematology. Journal of Nematology 31:93-94

Thursday, December 27, 2007

Circus of the Spineless #28: For the Benefit of Mr. Taylor

Christopher Taylor has posted the 28th edition of the Circus of the Spineless and set it to the tune of the Beatles' For the Benefit of Mr. Kite. Its a fabulous edition, naturally with an article from yours truly in it (plus a reference to Anthozoa Week!). So get your reading in before the end of the year!

Work With an (Virtual) Invert! - Biodiversity Informatics in Finland

The GBIF Node at the Finnish Museum of Natural History seeks a biologist with interest in taxonomy and informatics for a 3-year research project. The purpose of the project is to build an e-infrastructure for resolving scientific names of organisms to facilitate biodiversity data use and data sharing in the Nordic region and beyond. Initial appointment will be up to 24 months using available NordForsk funding. Further continuation is pending on progress and success in acquiring the necessary funding.

The work requires designing and setting up a service on Internet that will issue globally unique identifiers for scientific names and the underlying taxonomic concepts based on the Life Sciences Identifier (LSID) specification, which has been standardized by the Biodiversity Informatics Standards organization TDWG and is recommended by the Global Biodiversity Information Facility (GBIF). The incumbent will work in a team consisting of a computer scientist and contributors in Nordic countries. Details of the project are described in

Preferred qualifications
* Interest in taxonomy and understanding of how scientific nomenclature works
* Awareness of international developments in biodiversity informatics such as TDWG, GBIF, Species 2000, etc.
* General interest in Internet and good computer skills as user
* Good communication skills, including good command of English and preferably knowledge of a Scandinavian language
* M.Sc level in education.

Terms and conditions
Employed as Ph.D. Student at the Finnish Museum of Natural History, P. Rautatiekatu 13. Other location at another Nordic GBIF Node, or working remotely, is possible and can be negotiated.

The salary for a doctoral student is based on level 2 of the demands level chart for teaching and research personnel. With the salary component based on personal work performance the overall salary range is 1678-2450 euros per month.

How to apply
Send letter of application, CV and contact details of one or more referees Hannu Saarenmaa, Finnish Museum of Natural History, P.O. Box 17 (P.Rautatiekatu 13), FI-00014 University of Helsinki. Applications are not returned. The application deadline is Monday, 14 January 2008 at 15.45.

For more information please contact Hannu Saarenmaa, +358 (0) 9 191 28688, hannu.saarenmaa::at::helsinki::dot::fi.

Work With an Invert! - Crab Ecology and Conservation


School of Marine Science, Virginia Institute of Marine Science,
The College of William and Mary, Gloucester Point, Virginia

The Willard A. Van Engel (WAVE) Fellowship was established to promote research in blue crab ecology and conservation. Individuals of outstanding ability are selected to conduct research leading to a Ph.D. or M.S. degree in the School of Marine Science of The College of William and Mary. The 3-year fellowship is available beginning Summer or Fall 2008 in support of graduate research on the blue crab in Chesapeake Bay, with emphasis on any of the following: environmental and biotic control of recruitment and population dynamics; marine protected areas; predator-prey interactions; and ecosystem-based management.

Questions regarding potential research projects should be directed to: Dr. Rom Lipcius (rom::at::vims::dot::edu,

The fellowship offers an annual stipend of approximately $18,000 plus full tuition, and research and travel funds for 3 years, dependent on satisfactory progress. A 4th year of funding is possible given significant progress towards completion of the degree. The fellowship may be initiated in Summer 2008 to allow the conduct of research prior to classes. Candidates must be US citizens and accepted to the School of Marine Science.


1. Submit an application to the School of Marine Science. Deadline for receipt of applications to the School of Marine Science is 15 January 2008. Application information for the SMS is available at Application materials may also be obtained from: Dean of Graduate Studies, Virginia Institute of Marine Science, The College of William and Mary, P. O. Box 1346, Gloucester Point, VA 23062; and,

2. Send a letter requesting consideration for the WAVE Fellowship and a resume by 15 January 2008 to: Roger L. Mann, President, WILLARD A. VAN ENGEL FELLOWSHIP, Virginia Institute of Marine Science, The College of William and Mary, P. O. Box 1346, Gloucester Point, VA 23062.

Quote of the Day

"If value judgements have to be made, let us hope that they are the values of earnest seekers after truth, rather than those of academic politicians."

- M.T. Ghiselin (2002) Species concepts: the basis for controversy and reconciliation. Fish and Fisheries 3:151-160

Tuesday, December 25, 2007

Tuesday Toon

Monday, December 24, 2007

Merry Christmas from The Other 95%

Linda, Elliot, Freya and I wish you all a safe and relaxing Christmas/whatever day! This photo was taken by friend, photographer and ex-neighbor Josh Kaffer.

Congratulations Mr. Barton!

You can tell everyone that B.A. after your name stands for Bad Ass. As in, you can whip out Darwin quotes faster than you can say

"I have called this principle, by which each slight variation, if useful, is preserved, by the term Natural Selection"
Word. Chuckie D also has a word of advice for you in your future prospects:
"As for a future life, every man must judge for himself between conflicting vague probabilities."
I also recommend to you and ANYONE considering graduate school to read this essay forwarded to me by my officemate, S.A.L.-P.: Should I Go To Grad School?

Anthozoa Week at DSN and TO95

Hello there friends of the invertebrates! Over at Deep Sea News, Craig is out for a week so Peter has highjacked the blog and called for Anthozoa Week. Well, we're not going to let him do it all by himself! We'll bringing you news and views from the world of Anthozoa. What is Anthozoan? Glad you asked!

Anthozoa is a class of in the phylum Cnidaria that includes corals and anemones, characterized by no medusa stage (i.e. no jelly) in its life cycle. The word anthozoa means flower (antho-) animal (zoa). So sit back, relax and read an anthology of anthozoa this week here and at Deep Sea News!

What better way to start the week than to head over to and learn more about anthozoan biology and research! (Photo above is from copyright 2004 by Vreni Häussermann and Günter Försterra)

Sunday, December 23, 2007

Elliot Speaks Invert

I'm training him well. First it was fly (although meant for butterfly) and now its octopus. We're working on anemone, but that is pretty advanced.

Friday, December 21, 2007

Sea Squirts, SLOSS and of Course Porn

Blogging on Peer-Reviewed ResearchCastilla et al. (2007) are reporting in a recent PNAS article an interesting property of sea squirt pornography and local oceanography. I know, I'm a frequent purveyor of tunicate smut, but this utter filth may have consequences in the debates surrounding marine reserve design. These authors studied the spawning behavior of intertidal tunicates (Pyura praeputialis, an invasive) from chilean coasts. What they found will make all decent folk turn their insides out. These filthy denizens of the seas let it all out together in a mass orgy. Oh the indecency. Are you sure the children are asleep and not watching over your shoulder? You may want to tuck them in before continuing on.

Sea squirts have mobile "tadpole"-like larvae whose role is typically dispersal since they do not feed. The also don't stay in the water column for too long, preferring to stick their heads to a rock somewhere (figure below shows larval metamorphosis).

So what happens when tunicate sperm and egg meet seawater? An explosion of bio-foam! This foam is created by surfactants in Pyura's gametes (see figure below). This reduces the surface tension of the seawater. So basically, sea squirts spawn en masse, the high amount of gametes in tidal channels releases a high amount of surfactants which react with the seawater and its associated protein debris creating foam, the surface tension is reduced so larvae are not carried out to sea, thus larvae are retained in the tidal channel! As simple as that. Castilla et al. (2007) document the effects this foam might have on larval dispersal ability by monitoring ping pong balls in the channels. When there is no foam present, they all head out the channels to sea. When foam is present, 50-60% of the ping pong balls were retained in the tidal channel (depending on ebb or flood tidal conditions).

A) Mass splooging of P. praeputialis. B) Sperm (SS) and egg (ES) suspensions left dripping in the intertidal. C) 2 meters of foamy splooge. D) Chilean researcher knee-high in sea "squirt" if you know what I mean... Fig. 1 from Castilla et al. (2007).

So what is the end result of this filthy, spineless mass bukkake? (That ought to bring in the hits!) Larvae are retained in the tidal channels resulting in massive colonies over several generations. They are not trapped here though since theoretically, as shown with the ping pong ball experiment, nearly half of the larvae escape out to sea where they can start new colonies in other tidal channels perhaps. But this suggests that other larval forms are also retained during foamy times. Hence this bio-foam acts as resistor to the current of larvae out of a particular channel.

This has some interesting connotations for the ever debatable Single Large Or Several Small (SLOSS) dilemma facing marine reserve designers. If rare or endangered species occur in such tidal channels, for instance, you would want to grant protection to that channel. It is acting as quasi-reservoir for recruitments. Populations would appear to build up in these channels (excluding all other ecological forces that determine population size like competition, resource availability, etc.) and proportionally send out more larvae with each generation. This research suggests that protecting individually foamy channels (those with gametes secreting surfactants, or channels with high protein debris content) would more sufficiently protect the potential source of larvae for a particular species of interest. You just need to find the right areas, the foamy ones.

Of course this opens up a lot of questions. As someone interested in communities and diversity. I would like to understand how surface tension reduction affects the structure and composition of communities in foamy channels and compare that to non-foamy channels. Or, how planktonic communities respond to this potential stress? Does the composition of the seston track the cyclic patterns of the foam production and tides? Is diversity higher in non-foamy channels because foamy ones tend to have a higher dominance (and lower evenness) of a few species like Pyura praeputialis. Does the foam and reduced surface tension, act a barrier to immigration for new species and recruits? Its a pretty interesting system and though I don't know the foam literature well, I get a sense that this isn't well-studied. I will be looking for a postdoc very soon.... (hint hint).
Castilla JC, Manriquez PH, Delgado AP, Gargallo L, Leiva A, Radic D (2007) Bio-foam enhances larval retention in a free-spawning marine tunicate. Proceedings of the National Academy of Sciences 104:18120-18122. doi:10.1073/pnas.0708233104

Happy 81st JoePA!

Joe Paterno, head coach of the Nittany lions at Penn State turns 81 today. Dude, your old. He's still running around like a madman on the field too! I wonder what his secret is?

We used to live near him and when Linda and I would walk our kids on the nearby bike path where he often walked himself, he would stop and smile at our kids. They received Joe PA's blessing. May they grow up to as fit as him at 81!

Thursday, December 20, 2007

Assassin Bugs Use Corpses to Avoid Predators

Blogging on Peer-Reviewed ResearchNot only can your prey give your nourishment and a full belly, it can also be a shield to protect you from predators! A recent article by Jackson & Pollard in the Journal of Zoology described an interesting study in which the ant-snatching assassin bug (Acanthaspis petax) makes a "backpack" of its dead prey to avoid being seen by its predator, the deadly jumping spider (Salticidae)! Masking to avoid predation is not a novel development. There are decorator crabs who will take just about anything and put it on its back (including other live critters), sea urchins will don mussel shells and some weevils will even grow fungi, algae or moss on its back. What I think is cool about this system is the use of "corpse camouflaging". Not only can it save you from starvation, it can save your butt too!

"...they capture prey by grabbing it with their legs, piercing it with their syringelike mouthparts and using the ‘syringe’ to inject digestive enzymes and paralysing saliva. The bug then proceeds to suck up the digested ant tissues from inside the ant’s exoskeleton. Once finished, the assassin bug places what remains of the ant, an empty shell, on its back. The ant carcass adheres because of fine adhesive threads that the bug secretes from its abdomen."-Jackson & Pollard (2007)
Now thats recycling! I think we can learn something here. Perhaps we should recycle our food waste into new and life-saving innovations. Hmm... what can we do with all those leftover lemon and orange rinds?

Figure 1 (from Jackson & Pollard (2007)): Two juvenile Acanthaspis petax: one without (left) and one with (right) a mask constructed of ant carcasses.

Jackson & Pollard (2007) demonstrated that Acanthaspis with corpse backpacks were significantly picked off less by jumping spiders. They tested this using 3 different jumping spiders: Hyllus sp., Plexippus sp. and Thyene sp. Salticids are vision-guided predators so they would not be able to detect the assassin bug by smell per se. Spiders were presented either with naked, or unmasked, bugs or bugs masked with the putrid remains of their last meals (see figure above).

The result is that hits by all three species of spiders significantly increased when bugs were unmasked, meaning that the corpse camouflage is a successful deterrent to predators. To test whether the size of the mask affected attacks, the authors made lures that either exceeded or were shorter than the length of the naked bug. The result was the same in all scenarios: unmasked bugs were attacked an order of magnitude more than masked bugs. Hence, prey size is not a factor and the disparity between masked and unmasked bugs is due to the shield of dead ant bodies in and of itself. The lures also helped to control for confounding variables of using the live bugs (motion, behavior and other sensory cues), lending strength to their study.

But why a mask constructed of ant corpses? Ants are not necessarily the best prey for many species and are well respected across the animal kingdom. Typically ants are chemically defended or behaviorally defended (think of the swarming behavior of some species of ants), making them a difficult prey item. Additionally, there's not a lot of meat there so the effort put in might not balance with nutrition received. The authors hypothesize that their data suggest
"... that the salticid readily detects the masked bug as an object separate from the background, but it fails to identify it as potential prey.[...] As most salticids may be averse to preying on or coming close to ants (Nelson & Jackson, 2006), the fact that the bug’s mask is normally made of ants may be important when the bugs encounter salticids."-Jackson & Pollard (2007)
It would be interesting to see how this behavior evolved, what genes turn on this behavior. Once the gene(s) is/are found, how does that gene's phylogeny map over more conservative (i.e. less selected) genetic markers like mitochondrial DNA? A cross comparison with other decorating species would be very interesting in understanding the evolutionary history that gave rise to decorating behavior and how that behavior became instinct that is rooted in the taxon.
Jackson RR, Pollard SD (2007) Bugs with backpacks deter vision-guided predation by jumping spiders. Journal of Zoology 273:358-363. doi:10.1111/j.1469-7998.2007.00335.x

Nelson, X.J. & Jackson, R.R. (2006). Vision-based innate aversion to ants and ant mimics. Behav. Ecol. 17, 676–681. doi:10.1093/beheco/ark017

Wednesday, December 19, 2007

TO95: The Return

I'm Back! And with science even! We are all moved into our new house (pictures later), got internet restored at home finally, most of my end of the semester/year stuff is taken care of and I got a case Leinenkugel at home. So there really is no more excuses. And in case you think I might have been idle while I was madly running about with my head cut off, I have been downloading and reading aaaaaaaaaaaaaaaalllllllllll sorts of amazing invertebrate research, so I got a lot news and views to share with you. So keep tuned!

Other developments? If you are attending the North Carolina Science Blogging Conference make sure to come out to our session in Real Time Blogging in the Marine Sciences, co-moderated with K-lo, Peter E, Ricky Mac and Ceph-dawg J, word. Attendance is already at max capacity but you can sign up to be on the waiting list. Check out the line-up too, its going to be a good conference!

Big developments are underway as I speak. Its all hush hush right now, but I just wanted to plants the seeds of anticipation.

Friday, December 14, 2007

Raise Your Pereopod if You Hate Verizon and Forced Internet Providers

So I'm still out of internet service at home (where I do my blogging). I was told by the Verizon employee that helped me when I transferred service to my new address we would have internet access Dec. 12. Well that glorious day came and lo and behold... no internet service. I called that night only to be told by the nice, friendly automatic woman's voice (after a shouting a series of yes and no's, account numbers, etc.) that she couldn't help me and I need to call back within normal business hours.

So I called the next day and was utterly dumbfounded. Apparently, my account was suspended without my knowledge and the Verizon employee(s) couldn't tell me why. So after being transfered between 6 people (from the US to India at least twice...), hung up on once and shuttled between tech support and sales multiple times I finally came to the conclusion that I needed to start a new account. Fine.

So I got shuttled to a new person who quoted me the lowest price of $21.99. My old service was $14.99! In order to get that rate I had to order service online. OK, but I don't have internet service... His advice was to go to a buddy's. Fortunately for me I still do occasionally go into work and can obviously access the internet there or at the cafes where I sometimes operate out of (or the bar like I am right now). Unfortunately for my wife, who has been without internet and email access for 2 weeks now, she stays at and operates from home.

So I ordered service today and assuming it went through like the website said, I should be back in business by Dec. 21st. But, their customer service was horrendous and their answer to difficult questions is to shuttle you to India (whose answer is to shuttle you somewhere else too) or hang up on you. I wasn't being rude, but my tone was probably annoyed after about the 3rd person. And to top it off, I can't get the $14.99 rate for DSL without a 2 year committment. Since I know that I will not be here for 2 years and they made no mention of the fees for early termination, I didn't want to take my chances so I went with the 1 year contract at $17.99, still cheaper than ordering over the phone for whatever strange reason.

But don't despair, I'll be back better than ever. My end of the year stress is (mostly) over so I have a bit more time to write. Of course this misadventure has caused me to botch up hosting the Boneyard last week. I sincerely apologize to those who submitted and were expecting the Boneyard to be posted. Brian at Laelaps will be hosting the next edition and I'll make it up when I get fully restored.

Thursday, December 6, 2007

Work With an Invert! - Clam Tree of Life Webmaster

Position Announcement Available Immediately

The Paleontological Research Institution is a not-for-profit educational and research organization located in Ithaca, NY. It is PRI's mission, with its Museum of the Earth and other programs, to increase and disseminate knowledge about the history of evolution of the Earth and its life.

Scientists at PRI, in cooperation with Field Museum of Natural History, Harvard University, and eight other international partners, have been awarded a five-year National Science Foundation grant to build the Tree of Life for Bivalve Mollusks (= clams). We are seeking a motivated, full-time WebMaster to work closely with our research and outreach teams to coordinate all aspects and maintenance of our web presence.

The Position: Tree-of-Life WebMaster

We have an immediate opening for a skilled person with good communication skills to join our not-for-profit team. Participate in the planning, design, implementation, and execution of website activities that will facilitate communication and data-sharing among 15 scientists from 11 different institutions around the globe, translate research results into retrievable knowledge for the lay public, teachers, and students, and produce and maintain web-based deliverables. This is a full-time, five-year position dedicated to the requirements of the grant and other IT needs of PRI.

o Excellent organizational skills
o 3 to 5 years of demonstrated proficiency in web design and implementation (please provide written project documentation and links to completed projects)
o Ability to work independently and in small groups, manage time, and meet project deadlines
o Must work out of our Ithaca, NY, office
o Start date January 2008
Seeking Skills:
o Project Management experience is a must
o Experience with SQL type databases (MySQL), PHP, HTML, *NIX machines
o Solid understanding of cross-browser/platform issues and coding solutions
o Familiarity with Joomla website design software and Mesquite evolutionary analysis software
o Salary to be determined, depending upon qualifications (please include salary requirements in your cover letter)
o Standard benefits package, including health, disability, dental
o Employee discounts for Museum programs and store
Email by 20 December 2007 your resume and cover letter to: pmm37::at::cornell::dot::edu
Use Email Subject: Tree-of-Life Webmaster

Tuesday, December 4, 2007

Spongefest '07

Image from BIODIDAC

The answer’s fairly simple: Sponges feed like Protozoa,
And haven’t any enteron like other Metazoa;

Their ‘gastral cells’ are clusters of primaeval Collared Monads,

And their bodies have no traces of muscles, nerves or gonads.

Even their eggs are products of choanocyte divisions,

And therefore carry with them Choanoflagellate traditions:

Flagellate or Amoeboid, with collars or without,

They still are Collared Monads—though certainly more stout.

Walter Garstang (1985) - The Amphiblastula and the origin of sponges in Larval Forms and Other Zoological Verses (University of Chicago Press).

The latest of the the Journal of the Marine Biological Association of the United Kingdom (JMBA) is entirely dedicated to sponges. I believe this is a rather historic event, I doubt if ever before there have been so many Porifera publications (44 articles, 437 pages) in one place at one time. I think every sponge biologist in the world is an author or coauthor here. According to Van Soest's introduction to the special sponge issue:
It is proper and fitting that the Marine Biological Association of the United Kingdom comes forward with a special volume in its Journal covering these various sponge efforts. Right from the start of the Association, way back in 1884, and up to the present, the Journal has published sponge papers on a regular basis. Sponge fisheries and sponge culture were subjects addressed repeatedly in the earlier volumes of the Journal by E. Allen, the first secretary of the Association (1896), G.P. Bidder (1896, 1902) and L.R. Crawshay (1915, 1939). Sponge epigones such as A. Dendy and M. Burton discussed taxonomy, faunistics and ecology in the Journal and contributed to the authorative Plymouth Marine Fauna (e.g. Burton, 1957). Continuing along these lines, the volume presented here unites a series of 43 articles covering a wide range of sponge biodiversity studies, without pretending to delimit past or future eras of sponge research. As such it provides an overview of current sponge biodiversity research at this moment in time, and with 21 nationalities involved demonstrates the strongly international nature of sponge diversity science.
And just in case you forgot how cool sponges are and how they are so important, Van Soest opens the whole shebang with:
Sponges are an integral part of marine benthic communities with a high-impact role in benthic–pelagic coupling processes, as an important source of food for demersal grazers and predators, as hosts of a highly diverse microbial biomass, and as bio-eroders. Sponges provide age-old (hygienic) services to humans and continue to be of interest in modern times as sources of an unprecedented array of useful substances.

Hey Windows Users, Stop Being So Fucking Wasteful reports:

(CNN) -- True or False: Switching from a Windows-operated computer to a Linux-operated one could slash computer-generated e-waste levels by 50%.

The answer is: TRUE

A UK government study in late 2004 reported that there were substantial green benefits to running a Linux open source operating system (OS) on computers instead of the ubiquitous Windows OS, owned by Microsoft. The main problem with Windows users was that they had to change their computer twice as many times as Linux users, on average, thereby effectively creating twice as much computer-generated e-waste.

The report, titled, "Office of Government Commerce: Open Source Software Trials in Government - Final Report" reported the following:

"There are also potential Green Agenda benefits, through reducing the energy and resources consumed in manufacturing replacement equipment, and reducing landfill requirements and costs arising from disposal of redundant equipment.

"Industry observers quote a typical hardware refresh period for Microsoft Windows systems as 3-4 years; a major UK manufacturing organisation quotes its hardware refresh period for Linux systems as 6-8 years."

Though I do use a Mac like any intelligent person does (not to be a wanker Mr. Paddy K), I also run Linux (just switched to the Ubuntu distribution thanks to Mike) running WINE, which can run native windows programs. I haven't tried it out yet, since I've been taking exams, moving and finishing up massive grading, but have heard good things. The stupid thing is the only reason I need a Windows operating system is to run Primer (for my research) and MEGA (for a class). I'm hoping with this open source option I can rid myself of the necessity of using the Windows platform. Though I love my Mac, I would love to be entirely open source, just like how I would like to have research published in open access journals.

Hey folks, lets just get it all out in the open and stop being wasteful.

Carnival of the Blue Lucky #7

The 7th edition the Carnival of the Blue is up at The Natural Patriot. Dr. Duffy has a fantastic collection of wonderful oceanic posts. Be sure to read them all, just like life in the ocean the diversity is tremendous!

Circus of the Spineless #27: Is 6 the Meaning of Life?

The Hawk's Owl Nest is hosting the 27th edition of the Circus of the Spineless! It is huge. I swear this getting larger each month. It gladdens my heart to see so much spineless writing!

Christopher at the Catalogue of Organisms is hosting December's Circus. Get your posts to him BEFORE December 26 as it will be going up a bit early so he (and we all) can enjoy the holidays a bit.

Saturday, December 1, 2007

Seeking BoneShell-Yard Submissions

I'm hosting the Boneyard this upcoming Wednesday so lets get those submissions roaring in! Show the world where diversity lies and who is most abundant in the fossil record, I need your help to make this one special. Lets make it the SHELLYARD!! Get those invertebrate fossils posts in ASAP. Oh yeah... (mumbling under breath) i'll take vertocentric posts too i guess...

Dissertation Blogging Updates

I've considerably updated the Introduction and Chapter 2 to my dissertation blogging series due to comments from my advisor. It is much improved from before. So feel free to check it out and let me know what you think!

We are also moving this weekend so blogging will be slow. With two kids now, we are cramped in our little ole 2 bedroom duplex that we have called home since we moved to Penn State. Its a great place, but not for a family of 4. We are going to be renting a beautiful home on Mount Nittany, with State Forest for my backyard, a 5 mile scenic commute and plenty of space (in and outside) for our little planulae to run around! Its a beautiful place and worth every penny more than we are currently paying in rent. All hardwood floors, a wood-burning stove, enormous kitchen with oodles of counter space and smart cabinet arrangements, a fire pit in the backyard, a BBQ area with a stove for heat, plus the former owner left us lots of furniture to use. Its almost like heaven, except that we spent all night tonight cleaning it up... Expect pictures once we're settled in.

Thursday, November 29, 2007

Insect Art

(Hat tip to Michael Barton over at the Dispersal of Darwin)

This week's edition of Nature is chronicling the art of Californian entomologist Steven Kutcher. Kutcher uses the most unorthodox of paint brushes, the insect, to paint brilliant hues with creative strokes.

"Kutcher controls the direction and movement of his arthropods — such as hissing cockroaches (pictured), darkling beetles and grasshoppers — by their response to external lighting.[...] Kutcher's art is more than just a novelty, because it reveals the hidden world of insect footprints. 'When an insect walks on your hand, you may feel the legs move but nothing visible remains, only a sensation,' he says. 'These works of art render the insect tracks and routes visible, producing a visually pleasing piece'. "
For more of Steven Kutcher's art, visit Bug Art by Steven Kutcher, where I found this beauty coauthored by none other than Gromphadorhina portentosa (hissing cockroach).

Starry Night

Wednesday, November 28, 2007

Ocean Sciences Meeting Abstract Accepted

My abstract for The Ocean Sciences Meeting was accepted for the Census of Marine Life (CoML) poster session. The meeting is one, if not the, biggest meetings for ocean scientists and I am honored to be a part of the CoML. The work I will be presenting was part of a taxonomic training award for new investigators (link has my final report in addition to information about the award for those interested) I received from CoML's Biogeography of Deep-Water Chemosynthetic Ecosystems project (ChEss). My abstract is posted below. If any readers are going to the meeting or in the Orlando area and want to meet up let me know!


K.A. Zelnio, E. Rodríguez, M. Daly, C.R. Fisher

Hydrothermal vents are deep-sea ecosystems rich in energy and bacterial primary production. Cnidaria are not abundant in the well-studied Atlantic or Eastern Pacific vent communities. However they dominate some microhabitats on the East-Lau Spreading Center (ELSC). We report on six undescribed species of anemones (including one new genus) and a zoanthid from the ELSC. Three of the species of anemone are only found in areas exposed to hydrothermal flow, and will occasionally colonize the shells of mussels that require exposure to hydrothermal fluid to support their chemoautotrophic symbionts. Two of the other species are only present in areas isolated from direct exposure to hydrothermal fluid and the sixth is occasionally found in both peripheral areas and near to sources of hydrothermal flow. The zoanthid is the first to be reported from a hydrothermal vent and forms dense aggregations on basalt in areas of weak hydrothermal flow. The diversity of Cnidaria in this western Pacific back-arc basin is considered in the context of anemone and zoanthid diversity, distribution and habitat use at hydrothermal vents, methane seeps and whale falls.

More cnidarians than you can shake a manipulator arm at! Photo copyright C.R. Fisher/Ridge2000.

Fish & Wildlife Service Reverse Endangered Species Rulings!

Score one for mopping up after corruption! reports that the U.S. Fish & Wildlife Service is reversing seven rulings

"that denied endangered species increased protection, after an investigation found the actions were tainted by political pressure from a former senior Interior Department official.

In a letter to Rep. Nick Rahall, D-West Virginia., the agency acknowledged that the actions had been "inappropriately influenced" and that "revising the seven identified decisions is supported by scientific evidence and the proper legal standards." The reversal affects the protection for species including the white-tailed prairie dog, the Preble's meadow jumping mouse and the Canada lynx."

Julie MacDonald, the USFWS deputy assistant director at the time, pressured scientists to alter their findings in favor of certain industries that would use the protected land in other ways (i.e. building development). The Union of Concerned Scientists stated that these seven reversals "does not begin to plumb the depths of what's wrong" at the wildlife agency and its implementation of the Endangered Species Act. They have collected 30 cases of direct interference by USFWS over the last 7 years. Including (my favorite) delisting the splittail, a fish found only the California's Central Valley where MacDonald owned an 80 acre farm. Hmm...
Also included is critical habitat designation for the only invertebrate considered in these reversals, the stunningly gorgeous Hawai'ian picture-wing fly or Nalo Kihikihi in hawai'ian (Drosophila heteroneura, above from USFWS website). The Center of Biological Diversity reports on the threats for this backboneless beauty:
"Seventeen or more species may already be extinct and as many as 50 may be in serious decline. The hammerhead, for example, formerly occurred at 16 sites on four of the island of Hawaii’s five volcanoes. It disappeared from every site and was feared extinct until rediscovered at a single site on the Hualalai volcano in 1993.

Hawaii picture-wings have declined because of habitat destruction and the loss of their host plants. Remaining picture-wing species are threatened by degradation of their habitat by feral animals and invasive plants, loss of host plants, predation by introduced yellow jackets and ants, cattle grazing, and fire."

Tuesday, November 27, 2007

Its CEMS Time Baby!

Unfortunately, I probably won't be able to find the funding to go since I using what I have to go to The Ocean Sciences Meeting and Benthic Ecology Meeting. But click on the banner below to check out what all is involved for the 5th Congress of the European Malacological Societies.
Provisional themes for the 5th Congress of the European Malacological Societies:

1) Present and future challenges of fisheries and molluscan aquaculture

2) From theory to practice: What we can do for freshwater molluscs conservation

3) Origin, diversity and phylogeny of molluscs. Where are we?

4) Biogeographical processes and patterns

5) Molluscs as ecological models: from local patterns to global evolution

6) A palaeontological's eye: diversification and extinction of molluscs

7) Terrestrial molluscs: the perfect models for island biogeography?

Check One PhD Milestone Off!

Just like Pono the happy face spider, I am as happy as a spider to pass my comprehensive exam and move on with my life. Of course, I was passed with conditions. I have to write 2 reviews in areas my committee felt I needed more background in before my defense: species concepts and how to the community ecology of my system relates to that of other well-studied systems. I agree with them and felt my performance was definitely sub-par, but it what it is and they feel if I correct a few of my deficiencies than I will have no problem finishing my degree. Looks like I'll be helping pay John Wilkins living expenses. All in all they were very supportive and asked good questions that got me thinking about my research in new ways. It was a terrifying, but good, experience.

Monday, November 26, 2007

Doomsday Scheduled Between 9 and 11:30 am

Dear Committee,

I offer you my head on a block. Please have pity on me and do not take it personally if I break down and cry at any moment during my comprehensive examination tomorrow morning. I beg of you to find it in your heart to find me worthy of donning the title "Dr." and joining the ranks of the academic elite. Remember that you too were one a graduate student. Let us forget the good ole frat boy days of initiation and progress to nurturing and random acts of kindness.

Sincerely, Kevin A. Zelnio

p.s. - Do you take cream in your coffee? Need some leaves raked?

Saturday, November 24, 2007

You Know You're a Father When...

... the first thing that comes to your mind when you see a mess is where the wet wipes are. Oh those wet wipes. So many uses! Its a good thing.

Friday, November 23, 2007

Kenneth Ernest Lee 1927-2007

It is with great sadness that the death of Dr. Ken Lee is reported. Born, raised and educated in New Zealand, he was at CSIRO in Australia since 1965. His research has focused on soil ecology and he was an expert biologist of earthworms, mites and enchytraeids. A well written obituary is published in the June issue of Biology and Fertility of Soils (hat tip to the Annelida Listserve). Here are some selected excerpts:

"Over the next 10 years he completed a monographic study of the earthworms of New Zealand, detailing the morphology, systematics and distribution of 178 native and 14 introduced species (The earthworm fauna of New Zealand. NZ DSIR Bulletin 130, 1959). Whilst global knowledge of earthworm taxa and distribution has developed since 1959, the theses advanced in this monograph still form the basis of our understanding of the relations between earthworms and soils. Just one native earthworm species has since been added to the New Zealand fauna!"

"His seminal book on earthworms, whilst highly relevant to his work and of great intellectual standing, was written at home ‘after hours’—an illustration of how his family supported his science."

"Whilst Charles Darwin’s 1881 book The formation of vegetable mould through the action of worms first documented the importance of earthworms and launched soil biology, it was Ken Lee who developed knowledge about earthworms, their ecology and relationship with soils and land use, making masterful contributions to soil zoology and to the understanding of the importance of biological contributions to soil processes on the global twentieth century scene. To quote from the Avant-propos written by Marcel Bouche for the 1985 book Earthworms: their ecology and relationships with soils and land use, “The work of K. E. Lee, which for the first time places earthworms on a world-wide scale in the economy of nature and humanity, takes up again a century later, in modern terms, the message of the great naturalist. By its critical analysis, its synthetic approach and its opening up of all relevant subjects that are accessible to rigorous understanding, this volume of K. E. Lee takes its place as the direct descendant of that of Charles Darwin”."

Thursday, November 22, 2007

The Squidtivity! Just In Time for Squidmas!

Forget Black Friday, head online over and pick up your Squidtivity for this season's Merry Squidmas!

(hat tip to Will over at I Wish I Knew for the Squidtivity)

Wednesday, November 21, 2007

Inverts Hit a Double! Inverts 5: Verts 2

As you may have heard, a "man-size" fossil sea scorpion was recently found in Germany. Though I focused on the reporting and not the cool science, Deep Sea News confirms that this is definitely a score for the invertebrates. With chelicerae as a big as a toddler, I am pretty sure I would be sliced in half, though I would put up a good fight... Unfortunately, the largest known arthropods are hypothesized to be wiped out large toothy armor-plated fish. So, I am forced to give a point to both parties.

But my friend over at Lunartalks (hat tip to Peter Mc from the Beagle Project) more than makes up for Eurypterids dropping the ball. He reports on Jelly swarms committing genocide at salmon farms off of Ireland and how it makes him really feel.

For those keeping track:
Inverts 1: Verts 0
Inverts 2: Verts 0
Inverts 3: Verts 0
Inverts 3: Verts 1

Dissertation Blogging, Part 5: New Species of Alvinocaris

In preparation for my comprehensive examination next week and because its International Dissertation Writing Month, I will be posting my thesis proposal as I madly try to finish it all in time over the next few days. Feel free to question, correct, nitpick, criticize (constructively, I'm in a fragile state right now!), comment, praise me and make suggestions for improvement. And yes, I'm freakin' out!!!!


A new species of Alvinocaris (Crustacea: Decapoda: Alvinocarididae) from hydrothermal vents at the Lau Basin, southwest Pacific, and a key to the species of Alvinocarididae

Alvinocaris sp. nov. on Bathymodiolus brevior. The little limpet is Lepetodrilus schrolli. Photo copyright C.R. Fisher/Ridge2000.

My coauthor from Station Biologique de Roscoff and I have described a new species caridean shrimp in the family Alvinocarididae. This family of shrimp was split off from the Bresiliidae in late 1990's and forms a monophyletic unit that is adapted to deep sea reducing environments such as seeps and vents. To date, no other alvinocaridid has been confirmed from a non-reducing environment. Our species is very characteristic from other alvinocaridids in the shape of the telson and armature of the pereopods, or the legs. I just got the reviews from this paper on Monday and will be making the revisions, therefore I will not go into too much detail until it is published. Expect a full blown review later, but until then here is the abstract as it was submitted.

Abstract: We describe Alvinocaris (have to wait till its published to see the name!) sp. n. from hydrothermal fields at the East-Lau Spreading centre (ELSC). This species is larger than other alvinocaridids at the ELSC and appears to preferentially inhabit mussel beds composed of Bathymodiolus brevior. A. (name removed) differs from all known Alvinocaris by a distinctive, deep notch mesially on the telson. Suites of morphological characters separate A. (na na nana na) from other alvinocaridids. We analyze the degree of morphological variation in A. (yakity yak) and affinities of the Pacific Alvinocaris. A. (can't touch this) is also fit into a phylogeny of the Alvinocarididae using the mitochondrial COI gene and phylogenetic relationships are discussed. A key to the species of the family Alvinocarididae is included with locality information.

Dissertation Blogging, Part 4: Vent Food Web Structure

In preparation for my comprehensive examination next week and because its International Dissertation Writing Month, I will be posting my thesis proposal as I madly try to finish it all in time over the next few days. Feel free to question, correct, nitpick, criticize (constructively, I'm in a fragile state right now!), comment, praise me and make suggestions for improvement. And yes, I'm freakin' out!!!!

Part 1: Introduction
Part 2: Seep Primary Production of POM
Part 3: Community Structure at Lau Back-Arc Basin Vents
Food web structure at the Eastern-Lau Spreading Center

Vent crab, Austinograea alayseae, lying in wait in a chimney crevice? The shrimp are Chorocaris vandoverae. Photo copyright C.R. Fisher/Ridge2000.

It is established that chemoautotrophic primary production is utilized other inhabitants of vent ecosystems. This is evidenced by stable isotope ratios and gut content analysis of selected non-chemoautotrophic fauna. Stable isotope ratios provide a powerful tool to understand trophic relationships based on the predictable fractionation of elements with trophic level. Coupled with mixing model, stable isotopes can show minimum input of a source of primary production into an ecosystem in relation to other sources.

In this chapter I propose to construct a trophic model of this nested (within substrate) 3-foundation species ecosystem. A paper currently in peer review gave hint at some differences in the combined use of carbon and nitrogen stable isotopes in separating out signatures between the three chemoautotrophic foundation species. I will investigate the carbon, nitrogen and sulfur stable isotope composition of whole communities to understand resource partitioning, trophic guild structure and food web interactions in the ELSC ecosystem. Selected fauna from the periphery of the foundation species’ communities will be used to study how chemoautotrophic primary production is utilized away from the source.

• Null hypothesis 1: There is no difference in stable isotope ratios between chemoautotrophic foundation species
o Response: carbon, nitrogen and sulfur stable isotope ratios
o Predictor: foundation species type
• Null hypothesis 2: Stable isotopes ratios will be similar between substrate types for each foundation species
o Response: carbon, nitrogen and sulfur stable isotope ratios
o Predictor: foundation species type by substrate type
• Null hypothesis 3: There is no relationship of associated fauna’s stable isotope ratios to that of the chemoautotrophic foundation species.
o Response: carbon, nitrogen and sulfur stable isotope ratios
o Predictor: foundation species type
• Null hypothesis 4: Stable isotope ratios are similar between trophic guilds (i.e. no apparent structure is present)
o Response: carbon, nitrogen and sulfur stable isotope ratios
o Predictor: trophic guild level
• Other objectives:
o Use a mixing model to determine percentage of vent-derived nutrients used by associated fauna, using the chemoautotrophic fauna as proxies for the vent end-member(s)
o Form a model of the food web and trophic guild structure.

Man-Sized Sea Scorpion Fossil Found In Germany

Picture from article with the following caption, "The ancient sea scorpion, at 2.5 meters (8 feet) in length, was bigger than the average man is tall."

In my inbox this morning was this interesting article from titled Scientist finds fossilized claw of man-sized sea scorpion. Naturally, I was curious about man-sized fossil arthropods! While the find itself is great, the reporting was rather amusing. Large things and fossils always draw out the creativity in reporting, although many of the clichés have been well worn-in through time. I could quote mine this till the cows come home! For instance the opening line:
"This was a bug you couldn't swat and definitely couldn't step on."
How cliché is that? Why is always assumed whenever a 'bug' is mentioned swatting and stepping usually ensue? The following line mentions paleontologists "stumbling" upon the find. As if paleontologists are just out bumbling around without a clue. The author negates himself later in the article by describing how detailed the fossil hunt was, including seeing dark patches in the rock that signaled to them a patch of fossilized organic matter.

Of course they do make themselves favorable by printing this quote from Simon Braddy, one of the studies coauthors (to be printed the next Royal Society's Biology Letters):
"Hundreds of millions of years ago, these sea scorpions had the upper hand over vertebrates -- backboned animals like ourselves."
This next quote bothers me, can anyone figure out why? I will send an Aliens of the Deep IMAX movie poster and NOAA Ocean Explorer sticker to a person selected by my excel random number generator from all the correct replies. Contest closes Friday, November 23, at midnight. Email responses to kzelnio:at:gmail:dot:com. The winning response will be published on my blog and I might quote mine other interesting replies at my own discretion. The rules are that I am requiring a minimum 250 to maximum 500 word short answer on why this statement is misleading:
"The research found a type of sea scorpion that was almost half a yard longer than previous estimates and the largest one ever to have evolved."

Tuesday Toon

And we thought we had the upper hand over the arthropods for millions of years. They were just patiently biding their time knowing full well we would destroy ourselves.

From Gary Larson's Bride of the Farside.

Tuesday, November 20, 2007

Dissertation Blogging, Part 3: Community Structure at Lau Back-Arc Basin Vents

In preparation for my comprehensive examination next week and because its International Dissertation Writing Month, I will be posting my thesis proposal as I madly try to finish it all in time over the next few days. Feel free to question, correct, nitpick, criticize (constructively, I'm in a fragile state right now!), comment, praise me and make suggestions for improvement. And yes, I'm freakin' out!!!!

Part 1: Introduction
Part 2: Seep Primary Production of POM
Community Structure Associated With Chemoautotrophic Foundation Species at the Eastern-Lau Spreading Center in Relation to Stress and Substrate

Only one paper has addressed the ecology here, published by Desbruyères et al. (1994) it was based on targeted collections and video observations of the North Fiji and Lau back-arc basins. More recently, Henry et al. (submitted) found significant differences between the physiological tolerances of the ELSC chemoautotrophs in laboratory experiments while Podowski et al. (submitted) have found significant differences in the in situ thermo-chemical environment associated between various ELSC community types including the three foundation species’ communities. Communities associated with A. hessleri are exposed to high H2S, low O2 and high temperatures, while communities associated with B. brevior are exposed to low H2S, higher O2 and much lower temperatures. The thermo-chemical tolerances of I. nautilei overlap these two extremes. This gradient is apparent in their stratification, often resembling a "bull's eye" pattern around a vent opening with A. hessleri at the center surrounded by I. nautilei and then B. brevior.

My work seeks to understand the structure of chemoautotrophy-based communities at the Eastern-Lau Spreading Center (ELSC) in greater detail through quantitative sampling of foundation species. Two main questions are guiding this research: 1) What is the role of substrate in community structure? and 2) Are communities associated with chemoautotrophic foundation species structured along stress gradients? The data I have collected to address these questions include biometric data and abundance, in addition to mass and shell volume of a subset of the three chemoautotrophic foundation fauna from each collection. All associated fauna from quantitative collections of each community type were identified, enumerated and weighed for biomass.

The first question is derived from the observation that there appear to be wider diffuse venting communities on andesitic substrate, whereas on basaltic substrates venting appeared more localized. These two lava types are closely related but differ in concentrations of metals (i.e. iron, magnesium, silica) and physical properties (i.e. permeability, fragility). Additionally, polymetalic sulfides created as a result of hydrothermal venting provide a third substrate, likely the most extreme with reference to temperature and exposure to metal, hydrogen sulfide and oxygen concentrations. Two of our four study sites are basaltic while the other two are andesitic, but sulfides occur at all four sites in the way “chimneys” (see picture below) though the ones I was able to obtain collections from are only from the two basaltic sites.

Hydrothermal chimney built up from deposition of polymetalic sulfides. Encrusted with vent fauna, dark snail appears to be all I. nautilei and mussel is B. brevior. Photo copyright C.R. Fisher/Ridge2000.

• Null hypothesis 1: Mussels are in the same physiological condition regardless of substrate
o Response: condition index (g AFDW/internal shell volume)
o Predictor: substrate type
[figure and part of discussion removed]
The data suggests that mussels from andesitic communities are in better physiological condition over basalt and sulfide communities.

• Null hypothesis 2: There is no difference in biomass and abundance of chemoautotrophic fauna between substrates
o Response: biomass (kg/m2) and abundance (No. of individuals)
o Predictor: substrate type
[figure and part of discussion removed]
Biomass was not significantly different between substrate and between site. Abundance is significant only between andesitic and sulfide substrates and weakly significant between Kilo Moana and Tu’i Malila. The null hypothesis is only weakly rejected in certain cases, perhaps due to uneven sampling or high variability within a substrate type or site.

• Null hypothesis 3: There is no difference in the diversity (excluding chemoautotrophic fauna) between substrates
o Responses: species richness, evenness, Shannon index, Fisher’s alpha
o Predictor: substrate type
[figure and part of discussion removed]
The use of the various community indices suggest that andesitic communities are higher in diversity and lower in dominance.

Null hypothesis 4: Community similarity is the same across substrate type
o Responses: presence/absence, abundance, biomass, trophic guild biomass
o Predictors: substrate type, community type
o Method: Bray-Curtis similarity cluster analysis, multi-dimensional scaling
[figure and part of discussion removed]
Andesitic sites cluster together with varying chemoautotrophic foundation species biomass, suggesting that andesitic communities of different heterogeneities tend to be assembled similarly. All sulfide communities analyzed are from hydrothermal vents at basaltic sites, which they tended to cluster together with. ABE has a lot of overlap with the basaltic/sulfide sites. Tu’i Malila has little no overlap with basaltic sites and little overlap with ABE, the other andesitic site. Kilo Moana, TowCam and ABE are all relatively closer together while Tu’i Malila is farther south and shallower. These plots suggest that distance may be more of a factor in determining community structure than substrate type.

The second question makes the assumption that each foundation species occupies a certain niche on a stress spectrum. As previously described, the work of Henry et al. (submitted) and Podowski et al. (submitted) has shown a well-defined gradient of thermo-chemical tolerance both in lab experiments and in situ thermo-chemical sensing of the environments occupied by the three foundation species. I will test whether their respective communities are structured according to foundation species thermo-chemical tolerances as a proxy for environmental stress. To do this, I assign the highest stress to communities associated with A. hessleri, intermediate stress to communities associated with I. nautilei and the lowest stress to communities associated with B. brevior. Several samples were either chosen as communities of mixed foundation species or discovered upon retrieval to be mixed communities. These communities are analyzed separately and considered as an intermediate between A. hessleri/I. nautilei and I. nautilei/B. brevior communities.

"Bulls eye" pattern of chemoautotrophic foundation species around a fissure with diffusive venting. Photo copyright C.R. Fisher.

• Null hypothesis 1: There is no difference in diversity metrics (excluding chemoautotrophic fauna) between chemoautotrophic community type
o Responses: species richness, evenness, Shannon index, Fisher’s alpha
o Predictor: foundation species type

• Null hypothesis 2: There is no relationship between diversity and biological characteristics of foundation species.
o Responses: species richness, evenness, Shannon index, Fisher’s alpha
o Predictors: shell length, shell volume, biomass, percentage of most dominant fauna

• Null hypothesis 3: There is no difference in the diversity, abundance and biomass of mussel communities between different physiological condition indices.
o Response: species richness, evenness, Shannon index, Fisher’s alpha
o Predictors: condition index (g AFDW/internal shell volume)

• Null hypothesis 4: There is no community structure across foundation species type.
o Response: presence/absence, abundance, biomass of non-chemoautotrophic foundation species
o Predictors: foundation species type

• Null hypothesis 5: Within mussel bed communities, there is no relationship between diversity, biomass and abundance of the associated community to the mussel’s physiological condition.
o Response: species richness, evenness, Shannon index, Fisher’s alpha
o Predictors: physiological condition indices

• Other objectives:
o Plot shell length frequencies to test if there are patterns to recruitment within and across site and substrate type
o Report sampling effort using rarefaction
o Test whether taxonomic diversity is significantly different across site, substrate and foundation species type
o Explore the use of additional multivariate techniques
o Compare results and species composition to other western Pacific back-arc basins to discern any patterns, as well as to other hydrothermal vent sites.

Literature Cited

Bergquist DC, Fleckenstein C, Szalai EB, Knisel J, Fisher CR (2004) Environment drives physiological variability in the cold seep mussel Bathymodiolus childressi. Limnology and Oceanography 49:706-715

Desbruyères D, Alayse-Danet A-M, Ohta S, Scientific Parties of BIOLAU and STARMER cruises (1994) Deep-sea hydrothermal communities in Southwestern Pacific back-arc basins (the North Fiji and Lau Basins): composition, microdistribution and food web. Marine Geology 116:227-242

Fisher CR, Childress JJ, Arp AJ, Brooks JM, Distel DL, Favuzzi JA, Felbeck H, Hessler RR, Johnson KS, Kennicutt II MC, Macko SA, Newton A, Powell MA, Somero GN, Soto T (1988) Microhabitat variation in the hydrothermal vent mussel, Bathymodiolus thermophilus, at the Rose Garden vent on the Galapagos Rift. Deep-Sea Research 35:1769-1791

Smith KL (1985) Deep-sea hydrothermal vent mussels: nutritional state and distribution at the Galapagos Rift. Ecology 66:1067-1080

Monday, November 19, 2007

Work With an Invert! - Beetle Systematics

Beetle Systematics

We require a highly motivated Postdoctoral Fellow to assist a
research team to conduct research on systematics of beetles
(Coleoptera), with specific emphasis on the comparative morphology
of beetles. The research will involve research, documentation and
scoring complex matrices of morphological characters and
participation in development of interactive keys to beetle families.
Field work within Australia will be required and extensive use will
be made of electronic data management, imaging and publishing
methodologies. The research will be based at the Australian National
Insect Collection.

The application deadline is 6 December 2007 with interviews in January 2008.

Here is a link to the application form and job description.

Saturday, November 17, 2007

Dissertation Blogging, Part 2: Seep Primary Production of POM

In preparation for my comprehensive examination in less than 2 weeks and because its International Dissertation Writing Month, I will be posting my thesis proposal as I madly try to finish it all in time over the next few days. Feel free to question, correct, nitpick, criticize (constructively, I'm in a fragile state right now!), comment, praise me and make suggestions for improvement. And yes, I'm freakin' out!!!!

Part 1: Introduction


This chapter is completed and under internal review right now and will be submitted soon. Hence, I will not go into much detail about it right now, you'll have to wait till it gets published! Below is the abstract for the paper:
A Stable Isotope Bioassay for Seep Primary Production of Particulate Organic Matter

Hydrocarbon seeps provide a rich source of chemical energy in the aphotic, nutrient-poor deep-sea. Yet it is unclear how much chemosynthetic primary production enters the pool of particulate organic matter (POM) that can be utilized by suspension-feeding taxa. To address these questions, tissue stable carbon, nitrogen and sulfur isotope content was analyzed from suspension-feeding taxa at a hydrocarbon seep community dominated by the methanotrophic mussel, Bathymodiolus childressi, in the northern Gulf of Mexico. Two end-member stable isotope mixing models were used to determine the relative input of seep-derived POM to photosynthetic-derived POM that is assimilated into the tissues of the suspension-feeding community. Our results indicate that seeps play an active role in the production of POM, which is assimilated by suspension-feeders. Additionally, we constrain possible sources of nutrients to the POM pool.
OK, a little of the basics. A methane seep is an area where natural gas and oil diffuse from reservoirs below the sediment naturally. The seep I studied is called a brine pool. All you need to know if that a brine pool is weird, like an undersea lake of brine (see picture below). Salt concentrations ~120psu or about 4 times the salinity of seawater. The geologic history is complex, but has to do with a salt diapir from the depths of the sediment that recharges the brine pool. Particulate organic matter (POM) cold be anything with an organic origin but not currently alive; bacteria, dead piece of meat floating down from the surface, fish poop, mussel pseudofaeces, etc. This is filter-feeder food. Though passive predators, such as anemones, can phagocytose (engulf) these particles and take up dissolved inorganic carbon (DIC), this is a minor part of their diet. They are after all predators. I hypothesize that they are eating zooplankton hanging around the seeps. Unfortunately, no one has yet to study the zooplankton at the brine pool, so I do not know they exist there, but past experience shows me that where there is energy there is zooplankton! The zooplankton do feed from the POM pool. Hence passive predators are consumers of the POM indirectly. This is becuase stable isotope trophic fractionation for carbon, sulfur and nitrogen behave in a predictable manner (with some caveats). Meaning, "you are what you eat".

Brine Pool NR-1 "shoreline" composed of the methanotrophic mussel Bathymodiolus childressi with a syntactic foam marker visible. Density of mussels is ridiculously high (rope on marker is ~50cm). Photo copyright Ian MacDonald (TAMU).

I basically picked off filter-feeders (barnacles, sabellids, serpulids, sponge) and passive predators (anemones and hydroids) from foam markers at the brine pool, a few hundred km south of Louisiana. These markers had been down there since the early to late-mid 90s and recovered in 2004. Plenty of time to get fouled up! After torturing them a bit, I ground them up and sent them to get their isotopes analyzed. Previous authors have already determined the surface phytoplankton carbon and nitrogen stable isotope values right over our study site and the sulfur isotopes are known to generally be pretty similar from ocean basin to ocean basin (unlike carbon and nitrogen). These values became the photosynthetic end-member into the model. Another previous study by a member of our lab had determined the tissue stable isotope values of all 3 elements for B. childressi at the same location. These values became the methanotrophic end-member. Tissue stable isotopes from chemosynthetic (sulfide-oxidizing) clams and tubeworms were used as an input for thiotrophy. Thiotrophic input was deemed neglible because there were no standing stocks of thiotrophic organisms, though sulfide concentrations were elevated in the outer section of the gigantonormous bed of mussels and mats of sulfide oxidizer bacteria. I included it in my model for good measure and the model agrees with me.

If you plot the stable isotope values of carbon against nitrogen, a nice nearly-linear continuum between methanotrophy and photosynthesis is visible, suggesting mixing of sources in the POM pool. To make a long story short, the model results suggest that seeps play an active role in contributing to the pool of available POM, something close to a quarter. More later when its published!

Thursday, November 15, 2007

Accretionary Wedge #3: Between a Rock and Squishy Face, Geology and Life

That is our sample size, our replicate number with 0 degrees of freedom. If you believe the most popular estimates, Earth is ~4.6 billion years old. For a long time only rock existed once the planet cooled. Out of rock came life. Perhaps not literally, but only certain raw materials were present to work with: Nitrogen, Oxygen, inorganic Carbon, Hydrogen, Sulfur. Perhaps metals provided the catalyst, perhaps the Flying Spaghetti Monster reached down to bless our planet with His noodly appendage. The answer isn't clear, but I can guarantee its written in the rocks.

Geology has had an intimate relationship with biology, a long term romance spanning at conservative estimate around 3 billion years. As the disciplines of each are concerned, they were inseparable until the mid-19th century. Both were included with the modern sciences and maths as the study of Natural History, a subset of Theology. Some might say that the discipline of Geology was born with the work of James Hutton and Alfred Gottleib Werner in the 18th and early 19th centuries. Later on with the work of Charles Lyell, which heavily influenced Charles Darwin's theory of evolution by natural selection, Geology became a subject to study in its own right regardless of other subdisciplines of Natural History. Several years after which Biology was separated from Medicine and Natural History with the work of Darwin and Thomas Huxley and many others that followed into the 20th century.

Life exists, establishes and persists with geology's permission. Natural disasters can wreak havoc wiping generations of establishment and millenia of adaptation and diversity. Yet out of the ashes rises the phoenix and life reestablishes and re-adapts, and modifies the geological environment. Lichens break down rock into soil, plants establish their roots and suck out minerals and add organic carbon, microorganisms and meiofauna recycle and mobilize nutrients in the soil, animals enrich the soil both while living and dead. In the ocean, microscopic organisms extract calcium and silica to form tiny houses. These fall to the ocean depths as they die. After several thousands of years, this ooze layers on top of itself hardening and combining with weathered rock debris to form the substrate of Earth's most extensive habitat, the abyssal plain. Life may exist by geology's consents, but with a price.

The submissions received for this edition vary widely on the theme but are all enjoyable reads! For any new readers to the Accretionary Wedge, it is a geology-themed carnival started a couple months ago. Click on the link in the last sentence to find out more about it and consider submitting articles and hosting future editions.

Like me, Brian from Clastic Detritus has to write his dissertation. We can't just blog our lives away right? It also doesn't pay very well, or at all... But he was kind enough to take a break and submit an article on trace fossils he has found while doing his research. Check out the monster Ophiomorpha!

Also blogging on dissertation research, I present the introduction to my thesis proposal in the first part of a week long series of Dissertation Blogging as I prepare for my comprehensive exams in less than 2 weeks (I have to keep reminding myself). Prepare to be amazed by hydrothermal vents at back-arc basins!!

Chris from Zoogeomorphology Brilliant Mediocrity avoided talking about his thesis research, but captures the essence of the theme posting how life interacts with and modifies its environment using examples from beavers and whales.

Chris #2 from Highly Allochthonous, already completed his dissertation, takes a "grand and sweeping look at Geology and Life" and discusses how the air breathe became breathable in a BPR3-certified article.

Christopher (not to be confused with a Chris) from the Catalogue of Organisms highlights beautiful New Zealand serpentine soils and the plants the establish there. In an earlier post, he discusses a recent Nature paper on continental collisions with this loverly quote:
"Great chunks of the planet's surface get ripped up by colliding masses of rock bigger than all imagining, at scales at which living organisms just become negligible."
In a related post from earlier this year, brought to my attention by Yami from Green Gabbro, Joseph from the blog Science, AntiScience and Geology discusses research suggesting that the geochemical influx from the building of Gondwana may have triggered the Cambrian Explosion. Unfortunately, it seems seems these geologists may have disregarded some important biological information

Brian from the newly sexed up Laelaps, professes his love of squishy things and waxes beautifully and poetically on Aldo Leopald, the Book of Job, and Charles Darwin.

Julia at the Ethical Palaeontologist uses volcano farts as a segway segue into a discussion of volcanism and the public perception of climate change.

From the very cleverly titled All My Faults Are Stress Related, Kim ponders the granitic soil and its properties that make those oh so delicious blueberries grow there and be so... delicious!

Neil of Microecos reminds us to take a close look around us in public buildings. Fossils are everywhere in architecture and monuments!

Although Harold at Ontario-Geofish *claims* it happened to a friend, he discusses why one should go the emergency room and not try to solve medical problems with beer, especially urinary tract infections. Though not scientific, I thought there were lessons to be learned for field researchers in there.

Thats all for for edition #3 of the Accretionary Wedge. Next month's Wedge will be hosted at GoodSchist and please go the Accretionary Wedge page to submit ideas for the next and further editions.