Thursday, September 25, 2014

Caving in Northern Alabama

     In May I felt the twinge of wanderlust that sometimes takes over me: I needed to get out into the wilderness, and see things others had not seen. Luckily I received an invite to do just that, even though it was in perhaps the most ordinary place on Earth - Scottsboro, Alabama. It was a place I knew little about, that perhaps few besides its own residents know much about. But this was a wonderful place; home to the southern most stretch of the Appalachians, it looks like something closer to the Smoky Mountains than the bayou. The fog is thick, the mountains tall and verdant, the air a refreshing cool. I was here to go caving and, of course, to look for cavefish.
            Louisiana has caves, but no cavefish - a great disappointment. Alabama has caves, and perhaps an undescribed diversity of cavefishes - a great surprise. I’d fallen in love with caves in Madagascar, where I had first encountered them. I had been wholly unprepared then. Those Malagasy caves, full of strange life – odd birds, angry eels, giant-white-hairy spiders, big snappy crustaceans - was so new and unknown that I thought I was in Conan Doyle’s ‘Lost World.’ Madagascar got me hooked on caves for life. When Dr. Matthew Niemiller, one of the world’s preeminent young cave biologists, invited me to “no-where Alabama,” I happily accepted.
A little blind cave crawfish. I did not eat it, but I thought about it.
            Scottsboro is relatively close to Tuscaloosa; home to our LSU football (if not academic rivals) at the University of Alabama. I stopped over to visit their Museum of Natural History on my drive up from Baton Rouge. I found their museum quite beautiful, and their fish collections (in another building) in a much better housing than my own. I was glad to see our rivals on their own turf; and I was quite envious of their collections space and the wonderful Randy Singer, their collections manager, who was showing me around. After that brief visit I continued my drive to northern Alabama. I knew I was in cave country when the thick fog rolled in, I started to see limestone in the rock formations, and my car was pushing the limits climbing steep mountain passes.
            Our target was Limrock Cave, and Dr. Niemiller and colleagues from Auburn joined me near there in Scottsboro. Auburn recently provided their fish curator, Jon Armbruster, with a new building of which I am also extremely envious. (I hope someone out there is getting the hint.) Jon brought along his students Pam Hart and Charles Stephen. I met up with them that first night and was amazed to learn that Charles had not only also went to McGill University like me for undergrad, but also the same tiny Macdonald College campus. He studies pseudoscorpions, of which I know nothing, to his and my great disappointment. These little critters are very cool, especially, like most other things, the cave adapted forms.
            After gearing up and a short hike we were at our target, Limrock Blowing Cave. It was pretty amazing. Rather than the homogenous setting I expected from a North American cave there was quite a lot of habitat diversity, with deep mud in some spots, long windy paths, cool clear water in streams and pools, boulders in collapsed sections (“breakdowns”), narrow passages we could barely squeeze through and great big stalagmite and stalactite chandeliers in large open spaces - and always that utterly complete darkness and silence. Thank goodness for our headlamps and spare batteries. I would occasionally turn off the light and sit quietly just to take in how very dark, cold and quiet it was. The entire cave was nearly 10,000 feet in length, with lots of odd turns, tight crawls, high waters, and cold temperatures to give you enough of a thrill to make you feel like you are on an adventure. But there were also a great many cave animals, wholly unfamiliar to me. We looked for everything, insects, crawfish, spiders, salamanders and fish. We found a great many of these. What we didn’t find are bats; there was plenty of evidence that they were once there in great numbers but they became extirpated due to the scourge of the deadly white-nose syndrome.
Charles in a tight spot.
            Earlier this year Matthew and I described a new species of cavefish from Indiana, that we named Amblyopisis hoosieri, the Hoosier Cavefish. This odd creature garnered us some press because according to some reporters it looks like the human male’s reproductive organ. It is also the first cavefish described from the U.S. in 40 years and its anus is positioned directly behind its head – an odd place even for a fish (some reporters dubbed this a “neck anus”). North America actually has a great many cavefish species, at least compared to the poorly known stygobitic fauna of the rest of the globe. Matthew, on the strength of DNA evidence noted that the cavefish from north of the Ohio River (in Indiana) were quite distinct from those from south of the river (in Kentucky). This evidence set up an easy species description based on morphology of the new Indiana species to distinguish it from the species in Kentucky. It was also pleasing to name a new fish species after the birthplace of American ichthyology. We named the new species, Amblyopsis hoosieri after the “Hoosiers” of Indiana University because the new species is found very close to IU and because David Starr Jordan had once been university president. Jordan is also the most recent common academic ancestor to most, if not all, practicing North American ichthyologists. (He also was a social Darwinist, and may have killed off the founder of Stanford University shortly after he took over as president of that university.) In addition, the first female ichthyologist, Rosa Smith Eigenmann, wife of another noted Indiana ichthyologist, Carl Eigenmann, were also at IU. We named the new Indiana species to make note of the strong influence of IU on American ichthyology. I wanted to collect some of these North American cavefish for the first time so I travelled to Scottsboro, Alabama.
Target organism captured.
            Again we saw a great many cave adapted species from salamanders, to blind pigment-free crawfish, to Charles’s pseudoscorpions, to machete-wielding-Alabama hill people. I wore a double-layered wet suit with kneepads, helmet and lamp and I was sort of prepared for the cold and darkness of the cave, still I was having too much fun to notice any discomfort. We were after Typhlichthys subterraneus, which oddly for a cavefish is found in a rather wide and disjunct distribution. We found only three specimens all within an hour time span of the five hours we were in the cave. Each capture was thrilling. These blind depigmented thumb-sized fish were not hard to capture once you found them: a quick flick of the dip net was enough to bag one. Being blind and not used to predators chasing them, they were basically sitting ducks. I had the privilege of being there when two of them were caught. (I can claim only a single assist when I whiffed after kicking up one cavefish out of the depths with my boots, and which Jon Armbruster deftly captured– he caught all three.) It was a great deal of cold, wet, fun.
            Scientifically, it is unclear the significance of these specimens as of yet and I should say this is a Master’s students project at Auburn. I can say I am hooked again on cavefish and have some interesting Mexican material I can’t wait to tell you about. I’ll save that for another time…..

Friday, July 25, 2014

Media pumps up a little girl’s science project then viciously takes her down. Leave this kid alone!

A week ago!

 This week!

This is my take:
A precocious little kid did a science fair experiment for her school. It received attention because it is on a dangerous invasive and because a child did the work. She likely got the idea for the experimental design from her father, who probably got the idea from colleagues.
            Because people are interested in the topic and it was such a slow news week (besides the three airplane crashes, Israel/Palestine conflict etc.) this thing went viral. Anyway, who wouldn’t cheer for a young girl who discovered something cool, novel, and useful at the tender age of 12. But just as quickly as some were there to praise our new rising star, so too were they there to take her down just as quickly. Unfortunately, in this case the star/victim is a little girl with an interest in science. The media just made her an example of the climate for scientists today and women in science in general. The media’s interpretation of science is at fault here too. The headline that made me flinch the most was “Did [used her name] steal a marine biologist’s study for her 6th grade science project?” What a despicable thing to use a child’s real name in such a negative heading. Shameful.
            The timeline from Christie Wilcox above is the best thing to read out there from this "story." Shame on the reporters who wrote this girl's name in their stories and made it sound like she “plagiarized” another person’s work. She did not copy someone else’s work, the worst case is if she didn’t mention the work done before her as much as she could/should have.  This is a child people. At least keep her name out of this. Maybe she made a mistake in remembering how she came up with this project certainly it was influenced by the work of one of her father’s colleagues and perhaps in reading all of this wonderful press she started to rethink where these ideas originated. When talking to the press we often build narratives from our scientific work, we all stood on someone else’s shoulders and on the works of those that came before us. What happened here was a little scientific progress by a child that turned into a wider cultural regression.
  I understand the concerns of Zachary Jud, the PhD student who feels his work was slighted. He deserves credit for his work, but here is the thing - people are talking about his original work because of this little girl. The original work is already published and already got a little press, it is great that people are talking about this project again. This little kid has brought a lot of attention to it. Did she intentionally leave the original research out of the story to make her science fair research sound even better? I don’t think so. Even if she did, she’s only 13 now and kids make mistakes sometimes, but especially when talking to the media. If you are a scientist that has ever been asked “How did you come up with this project?” you know that it can be a very tough question to answer succinctly and you sometimes leave out details about all the influences you had in the past that got you to that point. Now imagine answering questions like that when you were 13 with an adult asking you the questions.
If you want to blame someone here blame the adults, blame the media, but don’t blame a little girl who just was trying to do a little science she was interested in.


Sunday, July 13, 2014

Make the link between specimens and genetic products as transparent as possible. #collectingisessential

I think the biggest issue molecular systematists will face in the future will be the pervasiveness of many genetic sequences from misidentified organisms. Our inability to track down the actual animal, plant, or fungus that many of our published genetic sequences come from is already a huge problem. There are plenty of sequences on GenBank and other sources from which we blindly download sequences trusting that this COI sequence from Coryphaena hippurus is actually from a dolphinfish and not an actual dolphin. Although there are lots of checks and balances to make sure that sequence of COI are actually from COI, and that these sequences lack stop codons, there isn’t much to check the accurate identification of the source specimen (a.k.a the voucher). Very few of the millions of sequences on GenBank can be tracked back to an organism deposited in a collection. If you download that sequence of dolphinfish and put it in your phylogeny and it falls out somewhere really weird then you can do a blast search and it will tell you that it is actually probably from a dolphin (if that is the case). But most of us are working at a much finer phylogenetic scale. We are building phylogenies of genera, families, or orders. At this finer scale it is very easy for someone to misidentify a species. (Google images of species from your favorite genus and see how similar congeners are in appearance.) Sequences generated from a misidentified specimen can easily end up on GenBank and often in the phylogeny of the day, and they do.

A wise mentor of mine used to say that every museum label has a question mark after the identification. I would say the same about the identifications on GenBank sequences except the nice thing about the museum specimens is that an expert on the group can one day come and positively identify the species based on the specimens: Not so with most GenBank data. The sequence is out there and if you have the right genus and not the right species it is highly unlikely that someone will catch that error anytime soon. It is quite likely in fact that many others will continue using those sequences, inadvertently perpetuating the error.

My colleagues and I want to put the power of identification back in the hands of taxonomists. I think it is safe to say that most people uploading sequences to GenBank are not experts in the organisms they are studying. They are trusting someone else to do positive identifications for them or they have collected some tissue samples from something they think they know very well but they may not. I see studies all the time where the samples were collected, tissue samples taken and the animals, and the carcasses of those animals were discarded (rather than kept in a permanent collection). That’s really not good, and a waste. First of all names change all the time. What if the study species is later split into two species; which one was the one you collected? What is needed is an unbroken and transparent link between the voucher and the genetic data.

Based on our observations that few researchers provide a link between their genetic data and collections data, either on GenBank or in their publications, a few of us [Carole Baldwin (Curator at the Smithsonian), Larry Page (Curator at the Florida Museum of Natural History) and my student and I] got together and created a nomenclature that should help remind people of the importance of making the link between specimens and genetic products as transparent as possible. The nomenclature is called GenSeq and it works something like this: The quality (trustworthiness if you prefer) of any given genetic sequence is based on how likely the identification of the voucher specimen is correct.  In our nomenclature the highest ranked, best sequences come from primary type specimens, like a holotype. A holotype cannot be misidentified because it is the main specimen chosen to represent the species when it was first described. Sequences from the primary types are ranked as genseq-1, the highest ranking in our system, because those sequences are from specimens with the highest likelihood of being correct identified. Sequences from secondary types (other specimens used in the original description of the species and designated as paratypes or other secondary types) are ranked second, genseq-2. This is followed by specimens from the type locality (same locality as where those primary type specimens were collected), genseq-3. Specimens that are vouchered but not from the type locality or type series as above are in genseq-4. Most sequences from specimens positively identified and deposited in permanent collections will be in that fourth category. The last category, genseq-5, is for photo vouchers. Although not ideal it is sometimes necessary to release an organism that you have taken a tissue sample from (think of something really big, or very rare). Also photo vouchers are necessary in cases where specimens are so small that the body of the organism is destroyed in the process of sampling its DNA. In these rare cases a photo is the best you can do to keep a record for identifying the species in the future. (Read more about photo vouchers versus actual specimens on Twitter using #collectingisessential or (see our paper here); you almost always need more than a photo to positively identify most creatures.

Anything without a clear link to a voucher (specimen or photo) doesn’t get one of these GenSeq tags. We recommend that systematist avoid using genetic data from which the source is unknown or unrecorded (and therefore lacks a GenSeq tag). After all, wouldn’t you prefer to know all the sequences you used were from organisms that were correctly identified by an expert? In an age where there is so much data available from so many species it is time to be picky. If you can download a sequence upload by someone who ‘kind of sorta’ thinks it is from a coelacanth, or the one where the voucher was identified by an expert and the specimen deposited in a permanent collection (where you can check it yourself if you need to) - wouldn’t you always choose the latter.

Right now many systematist, whether they admit it or not, will just not use sequences in a phylogeny if they originally end up in a clearly “wrong” place on the phylogenetic tree. That isn’t very scientific. Knowing it is in the “wrong” place in the first place is subjective. Of course most systematists will do a blast search and try to find alternative sequences, but the point is that the most rigorous approach is to make sure the specimen it came from was positively identified in the first place. We hope this GenSeq nomenclature is a short cut to doing just that.

We have published the GenSeq nomenclature here. And below is a poster we are presenting at some meetings that gives an overview of the idea. We hope people use it (by including a table in their paper linking GenBank #s to voucher #s and adding these GenSeq ranks). Too often people write in their publications something like: “Sequences were uploaded to GenBank and correspond to JK123332-JK678738.” That sentence tells us almost nothing. Not only do we not know what specimen might go with which sequences, we don’t even know which species goes with which sequences. If you then go to GenBank and download those sequences you will have the species - but little else (most people do not report the voucher numbers, if there are any). That’s a shame and something we hope to change. So the take home message is: Always link your genetic data to your voucher’s information! 

 P.S. - the 'Journal of Fish Biology' and' ZooKeys' have added the GenSeq nomenclature recommendations to their Instruction to Authors.

Monday, June 30, 2014

Can’t wait to get back to Kuwait: Fishes from the Arabian Gulf

Bill Ludt, Jim Bishop and me in downtown Kuwait City.
From June 13th to the 22nd my PhD student, Bill Ludt, and I travelled to Kuwait to collect fishes for the LSU Museum of Natural Science ichthyology collection. (This was the 3rd trip that Bill and I have now made to Asia in the last two years.) Over my career I’ve made collections from much of the Indo-West Pacific but am lacking some critical Middle East collections. The Middle East is underrepresented in most fish collections worldwide and because many of the species from the region are poorly known there is a potential that some of them are new to science. When Dr. Jim Bishop invited us to go to Kuwait last year I knew it would be an opportunity we shouldn’t pass up.
            Jim Bishop is familiar to many people in the LSU community; he is an alumnus and a great sponsor of art and research at Louisiana State University. Jim has a wonderful enthusiasm about the work being done at the museum, and he has provided many specimens to our collections in the past. He is also one of the most cultured, kind, and energetic individuals I have ever met. Bill and I were lucky enough to stay with Jim and his wonderful wife Virginia at their home in Kuwait City. We frankly could not have figured our way out of the local airport without them, let alone find the fishes we were targeting. Kuwait is an interesting country with a rich and ancient history that was transformed by the unimaginable wealth that came about through the oil industry. All throughout the places we visited you can see this dichotomy between an ancient desert civilization and a transitioning modern society. The temperature was rarely below 100 degrees even at night, and frequently much higher - this was the desert after all, but the roadways were green with introduced shrubbery that was irrigated with desalinated seawater. Locals wore traditional Islamic garbs (abbeys for women, dishdashas for men) but there were also many expats from India, Syria and the West. It wasn’t always clear when we were seeing the real Kuwait or just the veneer around it.
Bill Ludt rocking the guitarfish.
            Our first days were spent going through the many collections Jim had already obtained for us. Through his work at KISR (Kuwait Institute for Scientific Research) he was able to arrange for specimens of notable material to be held for our visit. These specimens were collected by boat trawls in and around the Arabian Gulf (what we call the Persian Gulf) over the past few years. By the end of the first day we had already gone through hundreds of samples that were a very good representation of Kuwait’s ichthyofauna. Jim had meticulous notes for these materials and much of it was preserved in alcohol (rather than fixed in formalin) so we were able to take DNA samples as well. The majority of the materials that we brought back to LSU are these collections from KISR. We also made substantial collections from the local fish markets, which included material from Iran, Saudi Arabia and Iraq. The local fishmongers sold an amazing variety of species on a daily basis. Although the exact localities of this material will remain unknown it was nice to get additional material from around region. We also did some collecting of samples from the oceans ourselves going out at low tide to collect blennies, gobies and toadfishes from the sandy intertidal zone.
Mudskipper: a fish that doesn't mind being out of water.
We were also able to catch a few mudskippers on one of our last collecting days; these fishes are among my favorite animals to catch, and my least favorite fish to anesthetize. These fishes, which spend most of their time out of the water, are incredibly cute, with big bulgy eyes at the top of their heads and an expressive “face” that makes them look like muppets. They live in muddy areas and keep water trapped in their gills while they scurry about the surface building territories and escape routes. The mud they live in is hard to traverse and the larger individuals were in waist deep mud that made it impossible for us to catch them. We stuck mostly to the shoreline trying to catch smaller individuals. Even these small ones are amazingly adept at getting away. We saw hundreds of these mudskippers and ended up catching only about ten. We were covered in mud by the end of the day and the incredible heat made the conditions rather harsh but ‘mudskippering’ is always great fun.
            All in all we brought back close to 80 species from Kuwait and the Arabian Gulf and roughly 300 new tissue samples and close to 500 specimens. We also built an important relationship with the folks at KISR. Jim invited me to give a presentation there and my talk, “What We Learned from the 2010 Gulf of Mexico Oil Spill: and other projects from Louisiana State University” was well received.  We have also started some collaborative projects with researchers at KISR. We are trying to arrange making a short course in ichthyology that Bill and I would teach sometime in the spring at KISR, and hopefully we will try to sample from other parts of the Middle East as well. In fact this article is hopefully just the first of many we will produce from these trips to the birthplace of civilization.
A stonefish, the most venomous of all fishes.

Wednesday, April 23, 2014

Southern Fried for a Day - Collecting organisms to save their species

Check out my guest post for 'Southern Fried Science' - - this was in response to the Minteer et al. paper in Science that says we don't need to collect specimens anymore. Ummm... yes we do -

Collecting organisms to save their species


Tuesday, February 11, 2014

A Proposal for a New #Altmetric, the Influence Score, to Accompany the H-Index and to Help Evaluate a Scientist’s Impact on Society

The H-index is among the most widely used metrics for evaluating the quality and quantity of a scientist’s publications; but what about their influence on society? Here I introduce the Influence Score that can help an outside reviewer better understand a person’s impact not just among other scientists but among the general public and those outside of academia. If the ultimate goal is to evaluate a person’s true overall role as a scientist, I think we should be considering how they communicate with all people not just other scientists (which is the case with the H-index). The new index can be used to accompany the H-index, but also incorporates it. All elements of the Influence Score can be looked up through simple Google and Twitter/Facebook searches.
            The H-index can be easily calculated in Google Scholar, I prefer it to the Web of Science or Scopus because Google Scholar counts books and other
Fig.1. Google Scholar Profile Page Showing H-Index in Red Box.
non-traditional peer-reviewed publications: and it is free! To calculate the H-index you essentially count down the number of publications and their citations until the numbers no longer overlap. A person with an H-index of 5, has at least 5 papers with 5 citations. Read more
HERE to learn how to calculate the H-index.) Because a scientist’s main role is still to communicate their science among peers (via peer review), the Influence Score multiples their H-index by 100, and down weights the other elements, which are a little easier to accumulate (e.g., # of twitter followers).  I chose the H-index over say, total number of citations (which might be more similar to # of followers), because it is easier to calculate for a given researcher, especially one without a Google Scholar profile (Fig.1). 
            The other measures of the Influence score includes a measure of their visibility with the press (i.e, the Press Index or P-Index for short). Using Google News, one simple puts the person’s name in the search box and counts the number of articles that are found, which Google also does for you (Fig.2). Because
Fig 2. Red box shows Google News P-index.
Google News is only searching through a relatively recent window of time, few scientists will have much more than a few articles about them. Sometimes it is worth googling the person with “science” following their name, as I did for James Watson (e.g., “James Watson science”), to distinguish him from other news articles about people with the same name. This measure largely is to bump up those scientists truly making a social impact as newsmakers. That is without bumping them up too much, I’m trying to avoid giving too much influence to “celebrity scientists” that don’t do much science of their own. Therefore, I suggest that you divide the total number of search results of the Press Index by 100 so that this score is not completely overweighing the person’s academic accomplishments represented by the (albeit crude) measure of the H-index. Folks like James Cameron that are great promoters of science, but are best known for other things, are intentionally excluded here. If someone could separate press about science related activities from all others, they obviously could still be included. This is also the most dynamic element of the score because it can change so rapidly. Jane Goodall can skyrocket to the top of the list with the publication of a new book.
Fig.3. Twitter and Facebook Fan pages showing # of followers.
            The third part of the Influence Score considers your sway in social media (i.e, the Social Media Index or SM-index for short), specifically Twitter or Facebook. For someone on Twitter you get 1pt for every follower. For someone not on Twitter but that has either a Facebook “Fan” Page or Facebook “followers,” you get 1pt per fan or follower. You don’t get points for regular old Facebook “friends” because that isn’t necessarily measuring your scientific influence. If they have both a Facebook Fan page and a Twitter handle you only get points for whichever is the higher value. To learn more about the role of twitter for outreach read David Shiffman’s @whysharksmatter excellent article HERE).  As with the Press-Index you divide the total number by 100; again this is to allow the more academic H-index to still have some weight. The reason being that someone with 40,000 Twitter followers and an H-index of 0 might not really be more influential than a scientist with an H-index of 40 and only 4000 twitter followers.
            The Influence Score is then the total of your (H-Index X 100) + (Press index/100) + (Social Media-Index/100). I would round this to the nearest integer. All three can be discovered relatively easily through searches (e.g. GoogleScholar, GoogleNews, and a Facebook/Twitter search). Below I’ve compiled a list of some of the most well known scientists and have calculated their Influence Score. I’ve also added folks randomly that I admire that might not be the most famous folks but that I hope will be one day, I think adopting the Influence Score might help them get the recognition they deserve for the impact they have in society. This metric is imperfect: but I hope it is a good start.

I would like to thank Paige Brown @FromTheLabBench and her class #manship4002 for helping me figure out a more user-friendly way to compile this Influence Score. Also would like to thank Joshua Drew (@Drew_Lab) and David Shiffman (@WhySharksMatter) for their comments and advice.

H-Index x 100
Press Index /100 (total articles according to GoogleNews)
Social Media Index
(Twitter/or Facebook followers)
Influence Score
Stephen Hawking
Neil deGrasse Tyson
Richard Dawkins
Bill Nye
Jared Diamond
J. Craig Venter
E.O. Wilson
Steven Chu
Buzz Aldrin
Sean B. Carroll
Jane Goodall
Ed Yong
Jane Lubchenco
Jack Horner
Carl Zimmer
Amanda Vincent
Neil Shubin
David Attenborough
James Watson
Hope Jahren
Eugenie Clark
Eugenie Scott
David Shiffman
Sylvia Earle

Note: As always I would like feedback on this post and if people have suggestions for changes or additions to the metric. Please e-mail me at