Tag Archives: Biology

My First Week as an Intern at Fossil Butte National Monument

First off, I have to apologize for my infrequent posting on my site but I wanted to let you all know that I have completed my first week as an intern at Fossil Butte National Monument! Long story short, it was amazing and I’m so far having a great time at FOBU. Already, I’m doing many of the things that I always wanted to do as a park ranger (although to be clear I’m not officially one yet). Tours, fossil preparation, hiking, greeting visitors, and finding fossils neatly summarize my first week at FOBU. Now, to be honest, the experience is not all flowers and sage bushes, sometimes, it can get a little slow in the visitor center or at the Research Quarry but that’s not really surprising given FOBU’s status as a lesser known National Monument. In fact, I have already talked to several visitors who only know of the Monument because they were in the area and they wanted to check it out.

Now, what makes FOBU so special is its status as a Fossil Lagerstätte. A Lagerstätte is a fossil quarry that has either an exceedingly high amount of preserved fossils (like Dinosaur National Monument or La Brea Tar Pits) or fossils that are preserved in exceptional quality (think Burgess Shale). FOBU satisfies both of these categories by having an exceptionally high and diverse amount of fossils (ranging from fish to bats) that are preserved in excellent quality (skin impressions, flowers, feathers, coprolites and even cartilaginous bone). As such, FOBU paints a picture of a world quite different from its modern, semi-arid desert climate. A lake stretched across Wyoming, Idaho, and Utah, known as Fossil Lake, deposited the vast array of fossils. This lake was a semi-tropical paradise and was the home for stingrays, crocodilians, large soft-shelled turtles, early horses, palm trees, ferns, and much more. This diversity helped established FOBU as a national monument and is the reason why I’m here today and writing to you this article. I applied for an internship at a national monument via the GeoCorps program and FOBU was one of the monuments I had chosen. I had actually visited FOBU years ago and became reacquainted with it when I took a Fossil Ecosystems course last year and learned about its vast diversity. Needless to say, I was pretty stoked when I got offered the position. SO Here’s a list of the things that I have done and noticed in no particular order

-I started working on a fish at the fossil preparation lab. The setup is arranged so that visitors can see your work on a tv screen and personally ask you questions about what you’re doing. I’ve never worked on fish before so it was a bit awkward at first but now I’m getting the hang of it. It will be awhile before I get actually good at it though.

-I sworn in my first Junior Ranger! Her name was Sarah and I believe she was six.

-Most common question at the visitor center is “Where’s the bathroom” haha

-I never used a cash register before so that is surprisingly one of the more stressful things to learn although I’m somewhat used to it now.

Mioplosus Fossil

-Got to give some mini tours at the Historic Quarry and show some excited visitors some freshly excavated fossil fish. That was awesome. I even got a photo holding up one of the fish with some children. I even found a fish eating another fish! That was rad (although I didn’t notice that at first due to the fossil’s state).

Research Qua

-On Fridays and Saturdays, I work with another colleague at the Research Quarry although we only work when there are guests present. We have to protect and preserve the monument but at the same time we have to interpret and demonstrate paleontology so it becomes a bit of a paradox. When guests aren’t at the Research Quarry, we have to sit and wait for them to come up before we can continue.

-Saturday morning I gave my first two tours to a rock group from Logan, Wyoming. I eagerly volunteered for the tour and gave my whole schpeal to them. I got a round of applause from them at the end that, whether done sympathetically or not, was nonetheless appreciated! Some of the visitors told me that I did a good job afterwards. I still have things to improve on (I kind of faltered at the bird and plant fossils) but I thought I did a pretty good job overall. It was fuuuuun.

-It’s been surprisingly cool and rainy here. I have to sometime wear jackets in the middle of the day and it can get to the low fifties at night. I was told it was quite hot before I arrived.

-I’ve been cramming as much knowledge as I can about this place. Geologic history, park history, species’ names, or where to eat in Kemmerer, it’s kind of intense but at the same time, it’s easy to do considering I’m constantly exposed to the information. This video succinctly summarizes my view of the whole thing. Fossil Butte View -We can hike off trail so I’ve been doing that more and more. I’m not exaggerating too much when I say that no matter where you hike in FOBU, you’re going to get a good view.

-Kemmerer, the nearby small town, has expensive grocery food but the liquor is at a reasonable price, take that for what you will.

-I live in fear of running over the cute, fat prairie dogs. They stand by the side of the road, on the verge or running across the street despite the approaching vehicles.

-Internet is very scattered out here but I can get wireless access at the local public library and, of all places, a Mexican restaurant called Taco Time. God bless you Taco Time and your so-so burritos. That’s all for now! I’ll write updates every now about my experiences here and I will try my best to continue on my usual articles. Until next time!

Screaming Nostalgia: Waiting for the Cicadas to Return

Nothing screams nostalgia like cicadas for me.

Yes, that’s right, the 17 year cicadas (Brood IV) have returned to my hometown in Kansas.  Although their love screeching has died down only last week, I already miss them dearly.  I was eight years old when they last showed up and I was terrified of them.  I remember their cries and I remember their shells, but most importantly, I remember being pelted by them the moment I stepped outside.  I was terrified of them as you couldn’t go a meter before a cicada would fly haphazardly into your face like a drunken moth.  I refused to go outside after the first few attempts.

It’s funny that pure, childhood terror has transformed into complete fascination with life’s derpy animals.  I love the hell out of these guys whether they are the seventeen year or the annual brood (the “dog days” cicadas) that we get.  Summer doesn’t seem right without these animals filling the humid evenings with their songs.

My love for them have even transcended over to video games to which I’m of course referring to the Pokémon; Nincada and its evolutions Ninjask and Shedinja.  When I first played Pokémon Sapphire I would train a Nincada briefly (unique typing at the time) and would eventually move onto other Pokémon for my team.  In the Generation 6 games, I trained him again only this time training both Ninjask and Shedinja.

The fact that Ninjasks’ ability is “Speed Boost” makes it so funny in my head just imagining this huge cicada flying around all over the place and bumping into things. MEEEEEP.  Image from bulbapedia.

The Nincada evolutionary line is the Pokémonified perfection it has achieved in bringing cicadas into the Pokémon world.  Nincada looks like the nymph stage, Ninjask looks like the flying adult while Shedinja is the discarded skin of the molted adult.  Nincada is the only Pokémon to evolve into two Pokémon at once, a trait that even Eevee can’t touch.  What’s more, Nincada’s Ground/Bug typing is perfectly suited for the nymphs burial ground while Ninjasks Flying/Bug typing suits its flying stage.  But it’s the discarded Shedinja that seals the deal having achieved a Ghost/Bug type.  It’s perfect!  The shell still has its original form but now takes life as a new being!  How bizarre.  I love these guys so very much!

Pokémon aside, I have had a fascination with these insects for years now and I waited very patiently for them to finally come back.  When they did, I was ready.  For those who don’t know, I’ve been working at a plant nursery job for several summers doing general landscaping.  I was keeping an eye out for any cicadas that had crawled out of the ground when we were working on lawns.  I managed to get a few photos of their infestation.

Bunch of holes in the ground that tell where the nymphs lived

Bunch of holes in the ground that tell where the nymphs lived

cicada nymph

Caught a nymph that hadn’t molted yet

Managed to get one while it was molting

Managed to get one while it was molting

cicada shells

many of the nymphs molted on the underside of leaves

Cicada shells at tree base

A LOT of them were at the base of trees, this dog just loves eating them!

cicadas

Seriously, cicadas are basically all-or-nothing. They were either not there or they were everrrywheeeereee.

giggity

giggity

Cicada food

Yummy

During the height of their infestation, Mary and I went to a public event hosted by the natural history museum on cicadas.  There, we got to learn more about the cicadas and WE GOT TO EAT THEM TOO!  Students either fried them up, caramelized them, buffalo sauced them, or chocolate dipped them!  Oh man, I don’t normally eat bugs so I had to build myself up for that one.  I started off easy with the chocolate dipped one but then went into the buffalo sauced ones.  Then for dinner, I had some fried ones in a taco.  The best way I can describe them is that they’re a cross between a shrimp’s shell and a popcorn kernel.  Don’t know how else to describe it, it wasn’t bad though.

Man, these insects are very pretty.  Mary and I saw a girl who had a huge cicada tattoo on her back and it looked beautiful.  Cicadas have a very nice looking wing structure and they have these cute little black pupils in their huge red eyes.  They also have a nice color palate too with gold, black, and red complimenting each other nicely.  Now even am tempted to get a tattoo of one!

During my free time, I actively hunted for spots that had the highest concentration of them.  I found a few good ones where you could easily see them zooming around the trees and screaming their little heads off.  I made it a habit to find their favorite trees and pick up a few just so they could crawl around on my arms and head (I even was pissed by them a few times, haha).

 

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Now their music has died down and the females will soon lay their eggs.  I will miss them dearly.  Though we will always have the annual cicadas, I will miss the 17 year ones.  They are the best definition of nostalgia for me.  Something that happened, albeit briefly, in my childhood that had a lasting impact for the rest of my life.  A fear that transformed into fascination.  I love these animals so very much.  I look forward to seeing their offspring another 17 years from now.  And with that said

MEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEP

Evolution Flight Expansion and an Extinction Expansion Idea

As a paleontologist, I love the crap out of the board game Evolution.  Designed by a Russian biologist, you win Evolution by having the most successful (i.e., most populated) made-up species.  You can have more than one species who can even cooperate with each other to help you win the game.

A simple concept but it’s the animal’s traits that really seal the deal for the game.  Giving your animal “Horns” or “Hard Shell” can help deter would-be predators.  Giving your animal “Long Neck” or “Scavenger” can help them survive tough rounds when food supply is low.  Giving your predator “Pack Hunting” or “Ambush” can give your animal an edge over the harder-to-kill prey.  You can add or change new traits as you progress through the game providing you the ability to adapt to your opponents’ strategies.

This is a fun game to play and I know I’m not the only one who enjoys it.  Many of my friends who have played this game once or twice are immediately hooked by its simple but endearing concept.

But unfortunately, there are a few problems with it that I feel need to be addressed.

Let me start with a problem that occurs depending on who you play with.  At the beginning of each round you add food tokens to the Watering Hole and these food tokens are what your species eat.  If there are not enough food tokens for all the species, your animal can starve and potentially go extinct.   This is determined by the cards you add to the watering hold which can range from negative to positive numbers.  The problem is that many of my friends throw in positive numbers in fear of the watering hole running out of food tokens.  As such, the starvation aspect of the game is downplayed so much that it can cause the game to be imbalanced towards already highly successful species.

But some people want to watch the world burn and purposely throw in negative numbers making for more enjoyable and competitive games.  So this is a minor issue.

An actual issue I have is the runaway success between two traits that can be exploited easily.  In the game, if one of your species has the “Warning Call” trait, it prevents another one of your species to be attacked by your predator.  If you pair this up with the “Symbiosis” trait (a species prevents a smaller species from being eaten), then you get an unwinnable combination that is hard to stop.  Sure, you can get the “Ambush” card to negate the “Warning Call” trait but you still have to be bigger than the “Symbiosis” species in order to deal any real damage to it (not to mention the “Ambush” card is an uncommon card).

There are other traits (e.g., “Hard Shell” and “Defensive Herding” in particular) that can be exploited to various degrees but none are as effective as this winning combo.  More often than not, herbivores dominate the board game landscape even when the predators get the amazing “Pack Hunting” trait at their call.  It’s rare to have a predator that is actual top dog.

From boardgamegeek.com

If you’re a reader of my site then you know that I’m a paleontologist.  As such, as I’m playing through this board game with all my friends, I keep thinking what I can do to improve it, to refine it, and to enhance the quality of the game while embracing the awesomeness of evolution.  There are so many animal characteristics out there that can be exploited that this game hasn’t even touched like camouflage or flight.

And guess what!?!?  The creators behind Evolution are doing an expansion for Evolution called the “Flight Expansion!”  Not only have they gone back and refined the original cards, they also added so many new traits as well including flight, camouflage, keen eyesight, and more!  And oh my god the changes!

Oh. My. Arceus. Yes.  All the problems I had in the first game are now being addressed.  This kind of response to balance issues in board games is simply great.  I can’t wait to get this game.  The expansion is on Kickstarter right now.  We still got two weeks until this Kickstarter is done but don’t worry as they are already well past funding!  I was very happy I found out about the Kickstarter thanks primarily by blogger http://ohjoystick.com/

Okay, so the Flight Expansion looks promising.

But I want to indulge a bit in what I think would be a great Evolution expansion.

As I already briefly talked about, there can be a runaway effect in Evolution where one person’s species becomes so large that no other animal can take it down.  They can then just up their population count and continue to eat a lot of food prompting them to win the game.  The updated “Pack Hunting” trait can solve that issue thankfully but even still, I would like to see some change on a major scale.

Evolution has been greatly affected by extinctions from a local to a global scale.  Species survive, outcompete, or die out due to changes in their environment.  The ruling class dies and the underdogs rise up to take their place as kings.  The characters may be different and the setting may be new but the plot is still the same.

And so I say, why not have an Extinction Expansion for the Evolution Board Game?

This expansion can upset the game’s foundation to the point that people who may be succeeding during the game now find themselves in a dire situation.  Those who were struggling now have the opportunity to overtake their now weakened (or even dead) competitors.  The possibility of different extinction events affecting species with various sizes, populations and traits is amazing and I feel giddy just thinking about it.

So, how would it work?  The way I imagine it is that at the end of every round, an extinction event card is drawn to determine if an extinction has occurred.  3/4th of the time, nothing happens.  However, for that 1/4th of the time that something occurs, the players have to do what the card says.  Here are the ideas I came up with (and feel free to contribute or change anything).

Ice Age: If a species has a body size>4 or if a species has the “Fat Tissue” Trait then its population size increases by one.  Climbers go extinct (no trees).  Watering Hole’s food supply is halved.

Tar Pits: Every time a species with the “Scavengers” Trait feeds in the following round, their population size goes down by one.

Meteor Impact: Body size>4 goes extinct.  Watering Hole’s food supply is halved.

Desert World: All species’ population size goes down by two except species with the “Burrowing” Trait as their population size increase by two instead.  Watering Hole’s food supply is halved.

Plague: All species’ population size goes down by one.

Invasive Species: Species with three traits are too specialized and are outcompeted (i.e., goes extinct) by an invasive species.

Humans: If a species has a body size>4 then their population size is reduced by two. If a species has horns then its population is reduced by one.

 

Those are all of the ideas I have come up with at this time.  I know there are some more extinction ideas out there but I haven’t quite figured out how I should use them in the game.

The best part about this expansion idea is that I can make this all by myself!  Since it’s entirely separate from the board game and does not rely on any pre-existing cards, I can just make my own extinction cards and apply it here!  I have yet to test it out but I’m looking forward to it.

Regardless, this is a fun game and if you haven’t played it, you should, it’s highly entertaining, and if you have a few dollars more to spare, you should contribute to the Kickstarter as well.  Who knows, there may even be a second expansion next year (fingers crossed for Swimming Expansion)!

Pokemon in the Biology Lab

I’ve been teaching introductory biology labs for several semesters now and if there’s one thing that I learned it’s that you have a limited time to teach your students the current week’s material before they get bored. Most of the time, this is not an issue as students have already become familiar with the topic thanks to the lecture. As such, lab lecture is more or less reminding students of the material and less of teaching them something new. After a short introduction we get right into the lab and have some fun.

But for the times when the lab is covering something new, things can get a little tricky. I heard somewhere before that you have five minutes to teach your students the pre-lab material before they begin to zone out. Five minutes, unfortunately, is painfully short and as such, I try to mix things up as best as I can so my pupils can continue to remain engaged (one time I even dressed up as a Eukaryotic cell and asked my students what each of my organelles do to keep me alive).

Such as the case two weeks ago when we tackled the vertebrate diversity lab. One of my favorite labs ever, the students were divided into three groups and each group dissected three different vertebrates; a lamprey, a dogfish, a perch, a mudpuppy, a frog, an anoles lizard, a turtle, a pigeon, and a rat. These animals represented the numerous broad groups of vertebrates; agnathans, chondrichthyes, osteichthyes, amphibians, squamates, turtles, archosaurs, and mammals. The overall message for that week’s lab, through the dissection of the nine animals, was that vertebrates have all evolved from a simple body plan to accommodate their environment and lifestyles.

Now, on the whiteboard, I had drawn a simplified version of a vertebrate phylogenetic tree as provided to the students by their lab book. However, as I was talking about each group of animals, I would slap on a printed-out picture of a Pokémon as an example of that animal such as Eelektross for agnathans.

pokemon phylogenetics, vertebrates, pokemon

Yes, I know this vertebrate tree is highly simplified but this was the level of education the lab was focusing on for the students. The class textbook goes into greater detail about the intricate relationships. All images are from bulbapedia.

Eelektross is always the first animal/Pokémon I would use as it represents the first branch off of the tree. Immediately, once I place this Electric-type Pokémon on the tree, everyone sits up and takes notice. I like to think that I have jarred them out of their sleepy, spaced-out zone and thrust them into something that they don’t know about (if they’re not Pokémon fans) or have much interest in (if they are Pokémon fans). Even if they’re not familiar with Pokémon, I would give my students a real life example of that animal it represents (lampreys) and then explain what sets this animal apart from all the other animals in the small phylum. After doing so, I would continue to the other animal branches and elaborate what makes them so special all the while continuing to slap on example Pokémon on the whiteboard.

Besides doing this for comedic sake, I like to use Pokémon for two reasons. One, using Pokémon is a way to get students interested in the subject manner at hand. Many of my students are pre-Med or pharmaceutical majors and that’s totally fine. But here, at the doorstep of all that is biology, where students are exposed to so many different topics that they will never tackle again in their future, I try my damnedest to show them how awesome those weird and unique topics are even if they may be as seemingly uninteresting as plants or population genetics. I know I will not convince many of my students to change their chosen path in life but if I have just one student that just stopped and ponder briefly whether they should pursue another topic in biology because of my lab, then I have succeeded. Using Pokémon is just one of many ways I try to generate excitement of all that is biology (paleontology is another one as well, of course).

The second reason why I like to use Pokémon is that I try to encourage a friendly, welcoming environment in my lab. I like to have a lab where people can be themselves. My icebreaker question even sets the tone for my labs as I ask each of my students what they’re nerdy about. Let me tell you, this question is great as I get to learn so much from my students and I get to relate to them for that particular hobby at hand or a hobby that’s close to it. I even like to chat to them as the semester progresses about certain news that may pertain to their nerdy hobby such as a recent episode in Game of Thrones or a movie update for the Marvel Cinematic Universe.

Be yourself and be open to new ideas. As gimmicky as these may sound, I adhere to them like a barnacle on a hard substrate. I don’t know how well these two ideas have been picked up by my students, but I will say that they…I don’t want to necessary say “enjoy”…but certainly like my labs judging by my evaluations. I hope though in the long run, maybe 10 or even 20 years from now, they’ll remember my lab lectures and one day recall, while playing Trivia Pursuit, that Mantine is a manta ray and all manta rays are chondrichthyes and then they’ll win the game! But I’m just fantasizing at this point.

Paleontology Misconceptions: Introduction, Megaloceros (the “Irish Elk”) and Orthogenesis

For the past few months, I have been stewing over what kind of paleontological articles I could write for my blog.  It’s easy to write and talk about comics, cartoons, and video games as you rely on experience and personal opinion.  Scientific articles, however, are more difficult for me as not only do they have to be interesting to the reader but they also have to be more objective and lean more heavy on up-to-date resources.  However, while I was sitting in the back row of the Introduction to Biology course (part of my requirement for being a lab TA), I was struck with an idea that was brought about my cool and collect professor.

In paleontology (and other sciences as well but I’m more attuned to the paleo ones) there is a large amount of misconceptions that many people believe to be true.  Some misconceptions are more innocently ignorant (pterodactyls and mosasaurs are dinosaurs) while others deceit even fossil enthusiasts today.  These misconceptions still hang around because they were long believed to be true, were over simplified, or were romanticized to the point that they have to be correct because it sounds so perfect.

Today, I adduce to you a fine example of a romanticized misconception.

Meet Megaloceros giganteus, a large mammalian deer that lived during the Pleistocene.  It’s also known as the “Irish Elk.”

And already, right from the get-go, we see two misconceptions that lead you astray from what this beast represents.

Irish Elk

The funny thing about Megaloceros’ common name is how plain wrong it is; Megaloceros is not exclusively found in Ireland and it is a deer not an elk.  First off, it can be found throughout Europe, North Africa, and well into western Asia (Lister 1994) so it has quite a diverse range.  Its association towards Ireland stems from its initial discovery there as well as the plentiful amount of specimens preserved in the Irish Bogs (http://www.ucmp.berkeley.edu/mammal/artio/irishelk.html and Gould 1977).  Irish poet Seamus Heaney even mentioned Megaloceros in his poem “Bogland” which is a short poem about the bogs of Ireland.

Megaloceros, map, distribution, biogeography, eurasia

Map from Lister (1994).

But being geographically confused seems trifling when many people assume that Megaloceros is an elk.  This doesn’t seem like a big deal until you realize that people in Eurasia use the term “elk” to refer to the animal that North American people refer as “moose.”  And THAT…is where the confusion lies.  Megaloceros is not a moose it’s a deer.  It was originally confused to be a moose because only moose were known at the time to have antlers that came even close to the size of Megaloceros (Gould 1977).

This moose-association was eventually taken down once enough viable specimens could be used for anatomical comparison.  Even the advent of genetic technology, which has the habit of shaking phylogenetic trees hard, did nothing to subvert this new-found truth and only enhanced Megaloceros’ position by placing it as a sister taxon to the fallow deer (Lister et al. 2005 and Hughes et al. 2006).

As such, many scientists nowadays call Megaloceros the “Giant Deer.” And though I think this name does not sound as majestic as “Irish Elk,” it is nonetheless 100% more correct and should be used more often.

But now let us get to the heart of the matter of the Giant Misconception for our Giant Deer.

You may be familiar with the Giant Deer in high school biological textbooks or as an example for Hardy-Weinberg sexual selection.  Similar to peacocks, males had large antlers to showcase their sexy fitness.  A display of dominance will win over any lucky gal and together, they can make adorable, small Giant Deer.

But.

For a long time, the prevailing hypothesis behind the demise of the Giant Deer was that their antlers were so huge that eventually their size drove them to extinction.  Their constant selection for bigger antlers meant they became too unwieldy, too energy costly, or just plain too heavy for the males to support.  Basically, the Giant Deer became too sexy.

This “Too Sexy for My Antlers” hypothesis was accepted as truth until the mid-20th century when paleontologists discredited it as being farfetched and countered that the antlers were the right size relative to the Giant Deer’s body (Gould 1977).   However, no one bothered to test this new hypothesis out!  This was until famous paleontologist Stephen Jay Gould stepped in and experimented with the hypothesis himself in 1973.  In his simple experiment, he analyzed modern deer specimens and compared the size of their antlers relative to their shoulder height.  He then compared his data to that of the Giant Deer.  What he found was that the antlers were not as dangerously large as everyone once thought they were.  In fact, they were at the expected level if you were to have a modern day deer of that size.

Photograph of Stephen Jay Gould from The Simpsons.

The importance of Gould’s discovery goes farther than determining the antler size of an extinct deer.  It discredited a long dead notion that continued to propagate the “Too Sexy for My Antlers” hypothesis.  There was this “theory” that existed in the late 1800s and early 1900s called orthogenesis that some scientists used to counter Darwin’s Theory of Evolution (and btw, before I forget, happy early birthday Charles).

Instead of Natural Selection, species evolve in a direct, linear path.  Species are evolving to a final end product that they are destined for.  As such, some orthogenesis scientists used the Giant Deer as an example of evolution that went too extreme and killed the species.  Taken from Gould (1977), orthogenesis supporter and paleontologist R. S. Lull said “Natural selection will not account for overspecialization, for it is manifest that, while an organ can be brought to the point of perfection by selection, it would never be carried to a condition where it is an actual menace to survival…[as in] the great branching antlers of the extinct Irish deer.”

Gould’s experiment was the final nail in a long-forgotten, already decaying coffin.  It was evidence that took down a dying idea that stubbornly eked out a living for many decades.  And yet while the scientific community had learned the new ideas and rejected the old ones, I would beg to differ that the public had been so quick to adapt as well.

Even I, who was a paleo-nut in high school, assumed that the Irish Elk died out due to its impressive antlers.  No one had bothered to correct me that it had a diverse geographical range, or that it was technically a deer, or that its antlers were the right size until I was a graduate student.  I would even go far as to argue that I was unknowingly accepting orthogenetic ideas while learning about biology and evolution.

I should try to get off my soap box before I become too preachy so I’ll end with this.  While writing this article, I was not aware of the orthogenesis hypothesis as I was never taught it before, even with all the biological courses I had taken.  I was taught Lamarckism and other discredited theories but never orthogenesis.  However, I think orthogenesis should be taught in basic biological courses as blooming scientists can learn what evolution is and is not.  They can learn why scientists thought orthogenesis is true and why it was ultimately rejected.  Learning about it can give a better understanding on how life works and why they should not accept this dead hypothesis.

And hey, if teachers were to educate their students about orthogenesis, students might even learn more about the Giant Deer and how, despite its outlandish appearance, it did not go extinct from being too sexy.

If you are interested in the crazy history of the Giant Deer, I recommend you to check out Gould’s “The Misnamed Mistreated and Misunderstood Irish Elk.”  It’s an enthralling read and greatly expands many of the concepts information I touched upon in this article.

 

Bibliography

Gould, Stephen Jay. “Positive allometry of antlers in the “Irish elk”, Megaloceros giganteus.” (1973): 375-376.

Gould, Stephen Jay. “MISNAMED, MISTREATED, AND MISUNDERSTOOD IRISH-ELK.” Natural History 82.3 (1977): 10.

Hughes, Sandrine, et al. “Molecular phylogeny of the extinct giant deer, Megaloceros giganteus.” Molecular phylogenetics and evolution 40.1 (2006): 285-291.

Lister, Adrian M. “The evolution of the giant deer, Megaloceros giganteus (Blumenbach).” Zoological Journal of the Linnean Society 112.1‐2 (1994): 65-100.

Lister, A. M., et al. “The phylogenetic position of the ‘giant deer’Megaloceros giganteus.” Nature 438.7069 (2005): 850-853.

He Died as He Lived: Karl Patterson Schmidt

It is not unusual for naturalists to die in the field, they are constantly exposed to dangers of all sort whether they be organisms, natural disasters, or even from man himself.  It’s also not unusual for naturalists and scientists in general, to be killed by the very thing they study.  Herpetologists have been killed by snake bites which would otherwise be not fatal had they been close to a medical facility.  Yet Karl Patterson Schmidt’s death is unusual for two cases, the first of which was that he died in Chicago.  Yet the second reason, and perhaps more interesting, was that he documented his own sickness as the venom took hold of his body.

Karl Schmidt was a prominent herpetologist in the mid-1900s.  He was president of the American Society of Ichthyologists and Herpetologists from 1942 to 1946, he was the zoological curator of the Field Museum from 1941 to 1955, and he named over 200 species of animals.  His prominence of the field is inarguable.

Yet despite his herpetological knowledge, he was bitten by a boomslang snake on September 25th, 1957 and died the following afternoon.  The boomslang snake, AKA Dispholidus typus, is a colubrid snake that can be found in Africa.  The boomslang has hemotoxic venom which prevents blood clotting.  The venom is stronger than other famous venomous snakes such as cobras and mambas.  Extreme care must be used when handling this dangerous animal.

Boomslang Snake

It begs the question why Dr. Schmidt was bitten by this lethal animal at the Field Museum of all places.  Well, he was supposed to identify the snake for Mr. Truett of the Lincoln Park Zoo.  When Curator Inger handed Schmidt the boomslang snake, Schmidt did not take the special precautions needed for handling it and was subsequently bitten on the thumb.

Schmidt and Inger were unalarmed by the bite.  The boomslang snake was very young and only one fang penetrated the skin 3 millimeters deep.  Schmidt shrugged off the bite but instead of moving on with his day, he decided, in true, scientifically enthusiastic manner, to document the nature of his health in response to the bite.

His “death notes,” for lack of the better term, were published by C.H. Pope in 1958.  And I have to say, after reading them, I am filled with forlornness.  Here was a man, enthusiastically documenting his health as it was deteriorating before his eyes without realizing that he would die soon. Dang, man.

Here’s an excerpt from one of his writings

“9:00 PM-12:20 AM Slept well. No blood in urine before going to sleep, but very small amount of urine. Urination at 12:20 AM mostly blood, but small in amount. Mouth had bled steadily as shown by dried blood at both angles of mouth.”

Schmidt is meticulous in his writings as he documents his temperature, diet, vomiting, and so forth at the time they happen.  As such, his writings give us a very unique and personal look at the effects of a boomslang bite while being objective about it.  Indeed, had Schmidt known that he was in peril, his documentation may have been rushed, confused, and mismanaged.

His notes stop the following morning when he thought he was getting better.  But after noon, he had troubled breathing and soon died shortly before 3:00 pm due to respiratory paralysis.  It is presumed from the autopsy report that his trouble breathing came from hemorrhaging in the lungs.  The autopsy also revealed hemorrhaging in the renal pelvis and the small intestine which accounts for Schimidt’s documentation of blood in his urine and bowels.

Dr. Schmidt’s death was tragic, but we gain much knowledge from it.  We now know of the effects of a boomslang bite and when they will happen.  But at the same time, I can’t help but think how much hubris Dr. Schmidt had.  Even when he was bitten by a known dangerous snake, even when he was witnessing the disastrous effects it had on his body, even when he was in reach of medical aid, he did nothing about it and died.  The irony stuns me.

If you want to read the death notes yourself then check out Pope C.H., 1958. Fatal Bite of Captive African Rear-Fanged Snake (Dispholidus).  Copeia, 1958, pg 280-282.  It’s a short but dour read that should be read by snake enthusiasts everywhere.

Too bad crocodiles can't fly, oh God, that would be terrifying. Imagine them crashing through your window.

Why Turtle Science is Good Science

Recently, in my Herpetology class, my professor informed us about a recent revelation in turtle evolution.  The turtles’ closest living relatives are in fact, birds and crocodiles (collectively known as the archosaurs to which I’ll refer to this as the archosaur hypothesis).  This is quite different from what I learned while growing up mainly that turtles were a weird outgroup of reptiles (see the figure below).  This was even commonly accepted in the scientific community.  Intrigued that a major shift in the Tree of Life has happened, I listened intently.

Too bad crocodiles can't fly, oh God, that would be terrifying.  Imagine them crashing through your window.

Possible phylogenetic relationships in Turtles. Tree A represents the traditional tree with turtles as an outgroup of reptiles. Tree B represents a different take using morphology as an example. Tree C represents the new tree with turtles a sister group to the archosaurs (the “archosaur hypothesis”).  Image from Hedges (2012).

The first papers that questioned turtles’ relationship on the Tree of Life were few and far between; some of which were even inconclusive.  However, Kumazawa and Nishida (1999), Cao et al. (2000), and Iwabe et al. (2005), were among the first scientists to question if turtles were actually a sister group to the archosaurs.  They had found strong evidence that this was so.  But, all three of these were either led or helped by Dr. Kumazawa meaning only a few scientists supported this hypothesis.  This changed in 2011 when we got a deluge of papers dealing with turtle relationships.  Shen et al. (2011), Crawford et al. (2012), Chiari et al. (2012), Fong et al. (2012), and Lu et al. (2013) all concluded that turtles were actually a sister group to archosaurs (this partially excludes Fong et al. (2012) who thought that turtles were either a sister group to lizards or to the archosaurs).

Again and again and again, we see continual support for the archosaur hypothesis from various different research groups analyzing various different genetic components.  I thought this was cool, but my professor by the end of his lesson seemed more annoyed then gratified by all this research.  Yes, alright, we get it, turtles are a sister group to archosaurs, move on.

But I had an appreciation for these scientists and their experiments.  This is science at its best.  We have rigorous testing of a novel hypothesis that has shaken traditional knowledge.  And through this rigorous testing, again and again, the hypothesis stands strong.

  If the actual ref was here, the turtle ref would have been used in kart racing.

This may seem odd to praise repeated testing, but lately, science, particularly pharmaceutical science, has been faltering lately.  If you have the time, you should definitely read the article here which highlights how repeated testing has taken a backseat in modern science.  Why is that?  Well, as the article states, it could be that the scientists want to make a name for themselves by testing new things, or journals may have no interest in repeated testing, or it’s just too costly.  Any of these could be a factor.  This lack of critical, unbiased repeated testing harms science as certain information we could perceive to be correct could actually be false due to human error.

This was why I was pleased to hear these multiple experiments done on turtle phylogeny.  It showed me that scientists are still questioning not just science but each other.  What’s more, the turtle phylogeny question has still not been accepted by everyone.  Morphologists, who study the structure of organisms, disagree with the archosaur hypothesis based on turtle anatomy and the fossil record.  However, even they have seemed to accept this hypothesis as the amount of research papers refuting the archosaur hypothesis has gone down considerably since the mid-2000s.  What’s more, I even found a morphological paper, Bhart-Anjan et al. (2009), which supported the archosaur hypothesis.

As such, in the space of about two decades, we see a great example of how our perception of science can change from one standpoint to another.  First, we have a generally accepted hypothesis (turtles are an outgroup of reptiles).  This was then challenged by a few scientists (turtles are actually relatives of archosaurs).  Finally, it ballooned to many scientists coming forth and supporting this new hypothesis through repeated testing.  To me, I find this awesome.  And that is why, my friend, turtle science, is good science.

 

Bhart-Anjan S., and Bever G. S., 2009.  An Archosaur-like Laterosphenoid in Early Turtles (Reptilia: Pantestudines).  Breviora 518:1-11.

Cao Y., Sorenson M. D., Kumazawa Y., Mindell D. P., Hasegawa M., 2000. Phylogenetic position of turtles among amniotes: evidence from mitochondrial and nuclear genes.  Genes 259:139-148.

Chiari Y., Cahais V., Galtier N., and Delsuc F. 2012. Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria). BMC biology 10:65.

Crawford N. G., Faircloth B. C., McCormack J. E., Brumfield R. T., Winker K., Glenn T. C., 2012. More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs.  Biology Letters 8:783-786.

Fong J. J., Brown J. M., Fujita M. K., and Boussau B. 2012. A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic Lissamphibia. PloS one 7:e48990.

Hedges S. B., 2012.  Amniote phylogeny and the position of turtles.  BMC Biology 10:64.

Iwabe N., Hara Y., Kumazawa Y., Shibamoto K., Saito Y., Miyata T., and Katoh K., 2005.  Sister Group Relationship of Turtles to the Bird-Crocodilian Clade Revealed by Nuclear DNA–Coded Proteins.  Molecular Biology and Evolution 22:810-813.

Kumazawa Y., and Nishida M., 1999.   Complete Mitochondrial DNA Sequences of the Green Turtle and Blue-Tailed Mole Skink: Statistical Evidence for Archosaurian Affinity of Turtles.  Molecular Biology and Evolution 16:784-792.

Lu B., Yang W., Dai Q., and Fu J. 2013. Using Genes as Characters and a Parsimony Analysis to Explore the Phylogenetic Position of Turtles. PloS one 8:e79348.

Shen X. X., Liang D., Wen J. Z., and Zhang, P 2011. Multiple genome alignments facilitate development of NPCL markers: a case study of tetrapod phylogeny focusing on the position of turtles. Molecular biology and evolution 28:3237-3252.