Thursday, March 19, 2015

Five Things you live with as a Taxonomist! Taxonomist Appreciation Day!

What are taxonomists? 
Simply put, taxonomy is the subsection of biology that deals with assigning names to biological entities and arranging them in an orderly "system." Usually in describing new species or even new genera, families or higher depending on what you work on. 

Many names apply and different scientists focus on different areas of expertise: Systematist, evolutionary biologist, invertebrate zoologist, marine biologist, paleontologist, systematic biologist, entomologist, botanist, protistologist, herpetologist, etc., etc. 

Arrangements of organisms are known as classifications which are dictated primarily by the evolutionary relationships of the organisms in they single celled amoebas, fungus, plants, or any number of animals..starfish, cats, water bears, fish, dinosaurs, etc. 

BUT the first part of that process is to figure out exactly WHICH species you are studying. What phylum of worm? What kind of single celled animal? What kind of plant?  Out of the hundreds to millions of known and unknown species in the world??  

Some species are well known, but others, especially those that live in poorly studied or out of the way habitats: the deep-sea, the distant tropics or even the microfauna and flora of your local pond these can be highly varied and you need a specialist to tell you what they are..(if you can't figure it out yourself!)

It was said for magic that knowing a demon or magical creature's name gave you power over it. This is the same for our knowledge of organisms. Knowing which genus, species, family, etc. allows you access to all the previously known knowledge about it. 

Do we have hundreds of articles on its biology? Or is it something completely unknown?


What do I do??
Even though I know a little bit about everything, my expertise focuses primarily on the diversity of sea stars, especially those in the deep-sea but you can read about me here.  There are other scientists who work on sea stars of course. Marine biologists, paleontologists, ecologists, and so on..  But at the moment, I am one of the only people who specializes in the evolution and identification of living sea stars (aka starfish or asteroids).

So, that's my bias.   

That said, I've been doing this for awhile now so here's a five ups and downs that I think I've experienced in my career as a taxonomist/biologist/paleontologist/whatever that I thought might provide some insight into why you should support a taxonomist (and taxonomy!)

As a taxonomist, these are dynamics that one comes to accept as part of the profession. They are challenges and we always hope that things will be better. But for the moment, this is how they are.. Most folks in the taxonomy field live with these things every day.

These are my opinions/perceptions and not the perspective of any organization I am affiliated with. 

1.  Taxonomy is biological infrastructure: everybody wants/needs what you offer but its often (still) professionally taken for granted.

For many decades, taxonomy was considered as almost a service to the rest of the scientific community. Say, you had some scientific study X, that focused on a weird deep-sea worm..but you didn't know what it was!!  Send it off to the local museum. Or to the Smithsonian or wherever.
They would often identify these things (and yes, of course for free) and there was not even a suggestion that the name of the taxonomist would be included anywhere but in the acknowledgements.

So, the scientists were held in high regard but never got full credit.
This happened to me a lot early in my career. but not any more...

TODAY, I usually insist on co-authorship on anything that involves a significant amount of work. Credit where credit is due.  

But, its still commonplace for papers that use one or many species to omit the name of the scientist (or whomever) who described it in the paper's references.

Its often convention to list the author and date of description after the species name, especially if it was described recently (i.e., in the last 50 years or so). This is usually done only in formal taxonomic papers. But in journals which use taxonomy outside of "formal" use (e.g., in ecology, physiology, etc.), its not unusual for the author and date to not be cited and the reference (and thus the credit) for scientific papers is denied to taxonomists. Thus lowering their status in the scientific community. This paper documents this issue. 

2. You get to travel.....but then spend months to years writing up the results

This is a good problem to have. Being a taxonomist has taken me all over the world and to the bottom of two oceans. You've seen my travel posts about working in Japan, Paris and out on ships to the middle of the North Pacific among the many places I've experienced and shared on the blog.

BUT these trips last for only so long. The exotic adventure stuff gets balanced by the more mundane preparation and wrap up. Some expeditions or even just museum trips take months to YEARS to completely "finish".
Why?  Most day to day work involves a lot of standard office work. Papers have to be written. Specimens have to be cataloged. Reports have to be made on the expeditions. Receipts have to be tallied. Meetings and responsibilites have to be met. Sometimes classes have to be taught.  For new trips.. proposals have to be written and logistics have to be made. 

So yes. cool things to be done and seen but a lot of the time. Work. Meetings. Etc. 

3. Most discoveries happen in museums....

I've written about this dynamic in past posts (here). Some specimens await discovery for decades before being found by someone who writes it up. On average this turns out to be about 21 years from the time the specimen is discovered until the paper is published..

As much as I've gone to sea and travelled to exotic places, I find the most number of new discoveries in buckets and jars of preserved specimens.

The museum is practically the HABITAT for the taxonomist. So, like any endangered species, one needs to save it to save the species!  If you support natural history and taxonomy, support the museum!! 

A lot of museums with natural history collections have also been struggling. Funding is almost always below what is necessary to maintain a collection at optimal levels. Other challenges to museums I've observed

  • Space! So many jars, specimens, etc. fit into a storage room and real estate can be expensive. Universities and private collectors are prone to give up their collections, which often end up at museums overwhelming the in-house resources.
  • Personnel! People are one of the most important ingredients to a good museum collection. Specimens require upkeep. They have to be cataloged. Shipped. Mailed. Received. Sorted. Some materials are protected by law. Training museum professionals is now its own field separate from what scientists do. Collection management is a challenge.
  • Resources! Specimens require material. Jars. Archival storage boxes. Tissue samples require freezers. Shelving. The list goes on. Individually, some of the items may not cost much..but remember these are used at a pretty regular clip.                                

and.. the resources above speak NOTHING of research materials.... DNA labs, microscopes, computers, etc. etc. which is another matter entirely.

4.  You belong to a small community which is growing smaller 
In this regard, taxonomy isn't all that much different from other academic fields or even other professional or business fields with a very specific focus.

Most taxonomists are unique experts in their group. As I said above, I am one of the world's only practicing taxonomists specializing in living sea stars (there are paleontologists around though). In the early 20th Century there were up to 5 to 7 sea star experts at any given time. Yes. there are people who work on regional faunas (i.e. starfishes of island X) but folks who work on all of them? That's me. 

For marine invertebrates, there is a perception that there is a serious lack of taxonomic expertise which I think bears some concern. You do get students who train and get degrees, but not a lot of jobs or positions are available. Some of us have gotten by but I've seen many of my gifted colleagues move on to other fields for lack of a stable position.

I've always seen the demand from other fields (ecology, physiology, oceanography etc.)  for MORE people who can ID or describe the "creature X" that they collected, etc.. but "Nobody works on those any more, since Dr. Y died..."

Which is a segue to...

5. There are new discoveries to be made!! but where are the jobs?
There are many places where you can read about the "Biodiversity Crisis" and the corresponding "extinction of taxonomists". Wired did a nice bit on it here. 

One of the things I always clarify to folks is that even though there's always something to DO, there's not always someone who will hire you to do it. 

I love what I do. But I don't have a "proper job" (I get by on soft money and other funds) but I feel compelled to continue (and I continue to hope!). My career is a good one but I've been lucky. Its a difficult field to survive in.

So, yes. There's an avalanche of undescribed species awaiting description! But whether you are a classical (but modern!) taxonomist like me, a person working on protists, or a barcoding guru, these are all pretty specialized positions. And getting a job doing what we're trained for is, at best difficult.

What happens when the last person working on a big or important group retires or dies?

There's been an unfortunate decline in jobs for taxonomists in recent years. This seems to accompany the various funding issues which accompany universities which have shifted their emphasis away from programs focusing on general knowledge.

Many reasons have been offered for this decline but ultimately I think the best I can do to support future generations and my other colleagues is to continue my outreach and shed a light on the challenges faced and why supporting taxonomists is worthwhile!

At this point, someone will bring up privatization or "Why don't you charge people for what you do?" And yes. Its crossed my mind..but that's a discussion for another post..

Wednesday, March 18, 2015

Pyritized Fossils! All that Glitters is not gold...sometimes it's MORE!

this image via Wikipedia
This week, I crack open my geology files and tell you a little about an interesting preservational process known as pyritization! 

This is actually a special type of preservation called permineralization, where an inorganic mineral "replaces" or forms a cast of a particular structure. Mostly hard parts, but soft parts are also replaced, as we'll see.

Pyritization involves the mineral iron sulfide (FeS2), (also known as pyrite or fool's gold)..which will replace the 'hard parts' (shells, skeletons, etc.) present on animals during preservation. 

This mode of preservation actually involves biology!! Bacteria, which are present during the decay of the original organism will produce sulfide. If you've ever seen something dead and buried, that rotten egg smell that accompanies the blackened tissue is the sulfide.

The bacteria in combination with minerals in the sediment/soil can lead to unusual conditions leading to the formation of pyrite which eventually becomes infused with the fossil, sometimes replacing the hard parts and sometimes even the soft parts..

Here are some neat examples...

Pyritized Devonian brachiopod! Paraspifier bownockeri. Image by James St. John

A Devonian goniatite (fossil cephalopod), Tomoceras unlangulare. Image by James St. John

unidentified pyritized ammonite

Some show exceptionally fine details!  Here are sutures on the shell..

And pyritized detail inside the shell

Endoskeletons and soft parts can also be pyritized, resulting in exceptionally preserved specimens!

Here is the Devonian Furcaster paleozoicus..a Paleozoic brittle star from the famous Hunsruck slate in Germany

A nice write up of this area, and the exceptional preservation seen there can be found on this website.                    .
A Pyritizied Devonian crinoid Arthroacantha

But probably one of the most exceptional examples of pyritization is when it captures soft tissues, such as on the trilobite, Triarthus

There were actually soft parts preserved on these trilobites, allowing for some fairly accurate reconstructions of the morphology...

Here's some with a size reference... the soft tissue preservation is remarkable...

and even trace fossils! Here's a worm tube with crystalline pyrite!

Tuesday, March 10, 2015

New Deep-sea Starfishes honor Hawaiian Scientists!

This week I talk about 2 new species of deep-sea starfishes from Hawaii described in my new paper published by Zootaxa

courtesy of Wikipedia! 
The paper has a very special meaning to me because it honors a scientist who was instrumental in getting my career started: Dr. Lu Eldredge, who passed away in 2013. 

Lu was a scientist at the Bishop Museum's Invertebrate Zoology department and was also the Executive Secretary of the Pacific Science Association

Lu had roots in the study of crustaceans but over the years had become sort of a polymath, studying everything from coral reefs to invasive species. A full pdf article of his scientific contributions can be found for download here.

Lu took a chance on me, early in my career and funded a visit for me to study the Bishop Museum echinoderm collections back in 1997 (or thereabouts). The funding was basic. I stayed at the YMCA and worked at the museum for about a month. No air conditioning. I ate at Zippys every day. Got lost on the bus pretty regularly, but swam in the pool every day. A difficult but fond time in my life.  

This was one of my first "real" museum visits and I learned a lot about being a research scientist and got my feet wet doing basic field work (we did some collecting) and studying museum collections.

While I was working, I found this specimen which I initially misidentified but later discovered was a species previously undescribed from Hawaiian waters.. A genus known as Astroceramus
The genus name is very descriptive. In the latin, "Astro" refers to the star shape and "ceramo" (or -ceramus) refers to "tile" So "Star shaped tile". This probably alludes to the very tile-shaped plates that comprise the animal's surface
And so, I have named this handsome starfish species for Lu : Astroceramus eldredgei which loosely translates to "Eldredge's ceramic star."

But there's MORE to this species than just a specimen!! The Hawaiian Undersea Research Laboratory has observed this species alive!! 
and more than that! they have observed it feeding on some of the deep-sea corals in the area.. Here is one image showing it feeding on the distinctive blue-colored deep-sea plexaurid octocoral, Astromuricea theophilasi
So, not only is it a cool looking beast but it is also likely an ecologically important one! and joins the ranks of the many other deep-sea corallivores I have written about...

A footnote about how new species often await "discovery" for YEARS before being found? The specimens described in my paper?  Date back to 1966! that's 4 years before I was born!

Lu Eldredge was a well-known and beloved personality within the context of biodiversity in the Hawaiian scene. There was a FULL volume of papers published in his honor published by the Bishop Museum which is summarized here. 

Among the other species named in Lu's name? SIX different types of crabs as well as an isopod and a coral...
  • Porcellanopagurus eldredgei, a bivalve-carrying Hermit Crab from Guam
  • Leptomithrax eldredgei, a new species of majid crab from Hong Kong
  • Forestiana lucius, a xanthid crab
  • Pseudomiccipe eldredgei, a majid crab
  • Petrolisthes eldredgeian Indo-west Pacific porcellanid crab 
  • Homola eldredgei, a homolid crab
  • Psammocora eldredgei, a scleractinian coral
  • Avada eldredgei, a parasitic isopod
Lu will be missed but through his work and his legacy he will be remembered.

Apollonaster kelleyi! 

I also honor another Hawaiian colleague, who remains very active with the Hawaiian Undersea Research Laboratory (HURL) and has been a great supporter of my work! Dr. Christopher Kelley, who is one of the primary scientists at HURL!!   Another bio of Chris can be found here.
from Nat Geo!
Chris does a lot. In addition to managing their video database, he runs any number of deep-sea and submersible projects and has done a LOT to further our understanding of marine resources (including fisheries) in the Hawaiian region.
From the University of Manoa page
You may recall that Chris has helped me with a few of my prior posts showing in situ images of various Hawaiian deep-sea echinoderms.  Such as this one with the asteroids and this one with deep-sea sea urchins

He's worked hard to provide everyone with a guide to Hawaiian deep-sea animals (here)! 

Apollonaster is genus in the same family as Astroceramus, the Goniasteridae. The name has an interesting history.. as it was named in honor of the Apollo 11 voyage which landed the first men on the moon. An apt genus to honor a deep-sea scientist!
Prior to this species being discovered, Apollonaster was known only from the tropical Atlantic! Could this be evidence that this was a species which occurred in both oceans before the closure of the Panamanian ishtmus??
A shallow water example of connectivity via a species occurring between these two oceans was detailed by one of my earlier posts on another sea star called Heliaster.

Wednesday, March 4, 2015

#sciart Who loves some cool ammonite art??

So, just got back from Japan and busy playing catchup and recovering from jet lag... so in the meantime, here's some cool ammonite art to go along with the #sciart hashtag currently producing such neat things on Twitter!

Paleoecology 19th Century style!

A wonderful piece by Ieuan Edwards!

with a cool "making of" pic..

This one is awesome!