Biochemical Soul Musings on Nature, Science, Evolution, Biology, and Education

27Jul/09Off

Beach-Combing Emerald Isle and Topsail Island, NC

(Note: As always, click image for better versions - these are heavily compressed)

Emerald Isle, NC

Last weekend we had a short but nice going away get-away with some friends (psychology graduate students, a parole officer, and a lawyer/rockstar) in Emerald Isle, North Carolina.

My dorky goal was to find more fossilized shark teeth (see previous awesome finds here), in addition to the obvious general goal of having a salty time.

Unfortunately, a storm kept most of the cool ocean debris from washing ashore until Sunday morning. Nevertheless, I found quite a few interesting things.

First off: fossil shark teeth!

Fossil Shark Teeth

Fossil Shark Teeth

The Haul:

The Haul 1

The Haul 1

The Haul 2

The Haul 2

The Haul 3

The Haul 3

Skate Egg Case:

Skate Egg Case

Skate Egg Case

Unknown wicked fish jaw:

wicked fish jaw

wicked fish jaw

Shell Fossils in matrix:

Shell Fossil in matrix

Shell Fossil Cast in matrix

Shell Fossil in matrix

Shell Fossil Cast in matrix

A cool fossil of what I think is a bryozoan.

Fossil Bryozoan

Fossil Bryozoan

I found a nice piece of fossilized bone. Of what? Who knows? Probably whale or dolphin. Or perhaps mermaid.

Fossil Bone

Fossil Bone

I also found several chunks of what I believe is either anthracite coal, or the next metamorphic step - graphite (I'm no geologist - thoughts?). It's very light weight, very hard, and very faceted - which doesn't come across very well in still shots:

Anthracite Coal?

Anthracite Coal?

Anthracite Coal?

Anthracite Coal?

One of the coolest things I found is a relation to organisms I will soon be working with in my new lab: starfish!!
I found two of these, both beautifully colored and still alive. They were washed ashore by the storm, so I tossed em back. I have no idea the likelihood of their survival, but I can say they didn't wash back ashore over the next two days. (I'm awaiting the expertise of Christopher Mah of the Echinoblog for species identification).
Update
: it's a Royal Sea Star, Astropecten articulatus. Quoth the EchinoMaster: "Basically..they are your stereotypical "sand star" predatory on infaunal bivalves and pretty common on sandy-muddy bottoms of the Northeast US.  Attractively colored animals to be sure!" Thanks Chris!

Starfish

Starfish

Starfish

Check out those details!

Starfish

Tube Feet Alive!!

We also got to hit the NC Aquarium in Pine Knoll Shores. It's a pretty rad place, so I was way more interested in pointing my eyes at all the ocean wonders, rather than pointing a camera. But I did get this cool shot of a gator.

Gator

Gator

Ooh - and apparently someone else took a shot of us there - me and John playing with the rays (the ray touch tank was by far the coolest part!).

Petting the stingrays

Petting the stingrays

Topsail Island, NC

A month ago, we also had the opportunity to hit Topsail Island, NC.

Fun was had. Things were seen.

Shark Teeth (Yes - I showed these before).

Fossil Shark Teeth

Great colors!

Fossil Shark Teeth

Ocean smoothed - but still pretty wicked

Mole Crabs (Emerita sp.)

Mole Crab (Emerita sp.)

Mole Crab (Emerita sp.)

Ghost Crab (Ocypode sp.)

Ghost Crab (Ocypode sp.)

Ghost Crab (Ocypode sp.)

And that's it - images are all I have for you at the moment. Enjoy.

I swear, I will have slightly more posts once I get moved to Pittsburgh and settled.

And just because I never show her (she's camera shy), I'm sneaking in this shot of my wife:

A Psychologist

Three Psychologists

7Jul/09Off

Mostly Expected Rhetoric from a Discovery Channel Exec

For those of you who don't know, David (WhySharksMatter) over at Southern Fried Science managed to snag an interview with Paul Gasek, Discovery Channel Executive.

David, as his handle implies, is all about sharks and shark conservation - in fact it seems he's been making quite a name for himself in sharkworld. Well, David, as well as many others interested in shark conservation (or even ocean conservation/health) have some issues with the way the DC's Shark Week continues to peddle fear of sharks. I've been personally pretty sick with most nature documentaries these days - catering to the 10 most deadliest this, or the Worst Disease You Can Get From that, or the Freakiest X, or the fear, fear, fear, etc...

David, based on many submissions from his readers, assembled quite an impressive list of questions (pulling no punches, I might add). I highly recommend you check out Paul's answers as it makes quite an interesting read. That being said, the answers were pretty much exactly what you'd expect from the exec of such a huge business as the Discovery Channel - and not all that impressive.

As I stated in the comments over there - it's all a bit moot to me, as I think the Discovery Channel bankrupted the "Discovery" in its name ages ago. Really - just look at the schedule on any given day. How much "discovery" do you see?

Edit: If you think this is a harsh assessment - keep in mind the titles of the first few shows for Shark Week when you read Paul's answers: the 2 hour premier "Blood in the Water," followed by "Deadly Waters," followed by "Day of the Shark 2" (about "when a great white breaks through a 300-pound aluminum shark cage and traps the divers inside. Another shark tackles a former Navy Seal in shallow waters"), followed by "Sharkbite Summer" (about "The bite-by-bite account of America's notorious "Summer of the Shark" in 2001.")

5Jul/09Off

A Tale of the Hunt for Fossil Shark Teeth

As someone who has been a lifelong fossil collector, I have a terrible, unforgivable sin to admit: I lived for eight years in North Carolina and never knew of the existence of Aurora, NC.

Mind you, since moving here for graduate school, fossil hunting had fallen off of my priority list, largely owing to the fact that central Carolina rocks are basically all metamorphic (melted and recrystallized by heat and pressure). And I've never been the gung-ho research-fossil-sites-and-go-hunting type. Since I began collecting while living in the Ozark mountains, it was more of a walk-through-my-parents-woods-and-see-what-fossils-I-find-today sort of hobby, with a few far-flung excursions in the mix.

Well that all changed a few weeks ago. My wife, some friends, and I spent a couple of days at Topsail Beach, NC.

Actually - scratch that - it began a few month's ago, when Christie at Observations of a Nerd reported an awesome find of fossil shark teeth in Florida, and then - like the wonderful person she is - sent me a handful of them.

Shark Teeth from the wonderful Christie

Shark Teeth from the wonderful Christie (Note to Christie - they are ray dental plates - not stingray barbs - just learned that - see below)

Back to Topsail Beach, circa a few weeks ago.

I said to myself, "Self - it's the ocean - there are bound to be fossil shark teeth. You (I) will not allow me (myself) to leave this beach without finding at least one shark tooth."

So I spent all my beach time on Saturday perusing the sands for teeth.

To no avail whatsoever. I never saw one.

The next day, I began again, searching much more intently. While combing the fresh tide-swept beach, I saw a tiny black triangle amidst the shells. It was a shark's tooth!!

The filters through which my perception is sifted were now calibrated. Within the next few hours I had a nice handful of tiny teeth. I was ecstatic.

(Note for the fossil pros and beach inhabitants out there: feel free to laugh at my ignorance of what constitutes awesome shark teeth. But these were just about the coolest things I had ever found - at the time.)

Hold your applause - you aint seen nothing yet

Hold your applause - you ain't seen nothing yet

Tiger Sharks - grrrr...er...meow

Tiger Sharks - grrrr...er...meow

Thus was I hooked on shark teeth.

The next necessary stops in my tale are the mountains of West Virginia and hills of Pennsylvania.

Some of you know that I will recently begin a new job at Carnegie Mellon University. As such, we have driven there twice recently. I am utterly awed by the massive amount of roadcuts through the mountains of the two states, all of which reveal millions upon millions of years of Earth's natural history in it's geological strata. I felt the fossil-hunting bug really kick up several notches while driving through those strata.

Thus, in anticipation of my move, I began hunting online for potential fossil sites in Pennsylvania. In this endeavor I discovered The Fossil Forum. Through this forum, I discovered not only a huge community of avid fossil hunters, experts, and enthusiasts, but also that North Carolina has some of the most amazing shark tooth sites in the country.

"Self," says I, "it's bad enough that you've been here so long without discovering North Carolina's fossil sites - but now you are leaving? I forbid you (myself) from leaving until you have visited these sites. Got it?"

It was decided - the July fourth weekend was my only free one from now until the move, thus I would make it a fossil-hunting weekend. I would spend Friday in Aurora, NC and Saturday at Green's Mill Run, a creek in Greenville, NC.

As fate would have it (though we will soon see that the result would have been the same with any weekend, fate or no) a dude by the name of MikeDOTB (Michael Taggert) on the Fossil Forum, was also making the exact same trip this weekend. We decided to meet at the shark-digging piles at the Aurora Fossil Museum on Friday (Note to parents in NC - TAKE YOUR KIDS HERE! Free digging teeth by the thousands to their little hearts' content). Mike said he would be there by 7AM and I would try to get there by 9AM (it's a 3.5 hour drive for me).

NOTE: See Mike's Trip Report here - he has some amazing shark teeth!

I was too excited. I couldn't sleep at all the night before. So I slid out of bed and out the door at 3AM arriving at the piles in Aurora by 6:30AM. (The piles are Pungo River Formation sediment - age ~18-22 million years -  donated by the nearby PCS phosphate mine).

It was just me. Not a soul in sight anywhere. Alone - in a beautiful dawn with giant piles of Miocene sediment to sift through at my leisure.

I saw my first tooth within about ten seconds of glancing at the piles. My collection grew fast and linearly from that point onward. Before too very long, a nice man showed up to sift as well. It turned out that he was a Fossil Forum member too (runner50) - a Kansas Science teacher on a trip around the country to spread his recently deceased wife's ashes at their favorite locations (including St. Claire, Pennsylvania which has some amazing fern fossils, which he showed me). Many of the ancient teeth he was collecting were for his students/class. Despite the sadness of his tale, it was incredibly heartening to meet such a man teaching in Kansas, a place we all probably know needs good science teachers!

In the wild

In "the wild"

Mike showed up later than he had planned, but as soon as he got there we hit another nearby pile, meeting a guy named Brian in the process. We chatted for quite a few hours as the three of us sifted for teeth in a couple different locations. Brian, another Fossil Forum member, gave me a dolphin vertebra among other things.

Dolphin Vertebra - Thanks Brian!!

Dolphin Vertebra - Thanks Brian!!

Fossil enthusiasts are awesome people, based on the few I've met!

Mike, Brian, and Me - sifting the piles in Aurora, NC

Mike, Brian, and Me - sifting the piles in Aurora, NC

Mike, showing how its done with his giant 1/2 mesh screen

Mike, showing how it's done with his giant 1/2'' mesh screen

The piles

The piles

I almost look like a real paleontologist. Or not...

I almost look like a real paleontologist. Or not...

Before the day was up I had amassed a huge pile of little shark teeth, though no lunkers had given themselves up. I had already watched in envy as Mike pulled several beautiful teeth from the piles. However, I wasn't really jealous, as I was too excited from the insane numbers of teeth I  was finding with my smaller 1/4" mesh screen. After about 13 hours straight (no lunch break or anything), darkness began to loom. So Mike decided to collapse the pile we had been digging into. Wet internal sediment began falling and we both began picking through it as more fell. In about a third of a second a shiny glint caught my eye in the muddy dirt. I snapped at it like a greedy hungry chicken.

It was a big Extinct Giant Mako (Isurus hastalis)!

Extinct Giant Mako make-o me happy

Extinct Giant Mako make-o me happy

Also, it had a small bit of feeding damage at the very tip (which makes it only cooler to me). Now go back and compare that to my first teeth from Topsail...

Without further ado, I give you the rest of my collection from Friday, filled with makos, tigers, sand tigers, snaggletooths, cow sharks, and even one small  nearly complete tooth and some pieces of megatoothed sharks (C. megalodon and/or chubitensis).

Note: I have zero tooth ID skills, so forgive any errors. There are almost certainly teeth "out of place"! I arranged these pretty quickly.

(Click for larger)

The Catch

The Multi-Million Year Old Catch

Arent they pretty?

Aren't they pretty?

A few of these were given to me by Mike - I don't remember which ones. Thanks Mike! He also gave me the coolest thing I now own...keep reading.

Tigers and Snaggletooths

Snaggletooths and Tigers

Sand Tigers et al

Sand Tigers et al

Megalodon/Chubiitensis?

Megalodon/Chubitensis?

Makos, Giant megalodon chunck, and others...

Makos, giant megalodon chunk, and others...

Lemon sharks and others?

Requiems, Coppers, Hammerheads? No idea...

Broken cow sharks

Broken cow sharks

Ray dental plates (for grinding munchies)

Ray dental plates (for grinding munchies)

The little guys (Mike estimated ~1200 total teeth)

The little guys (Mike estimated ~1200 total teeth)

Did you know a single shark can go through 30,000 teeth in a lifetime?

Did you know a single shark can go through 30,000 teeth in a lifetime?

And of course, I found some other cool stuff as well...

Shark Vertebrae

Shark Vertebrae

How cool is that?

How cool is that?

Coral

Coral

Love the detail in these things!

Love the detail in these things!

So I had a great haul - and searing back and arms as payment to Mother Nature for her bounty. But back pain or no, we had another whole day to go.

Mike and I high-tailed it to Greenville and crashed at the Motel 6, after spending at least an hour rinsing and gawking at our fossils. Mike gave me most of his teeth, except for the near perfect ones he deemed fitting for his collection. What an awesome dude!

Then again, this is a guy who has 30,000 teeth! Also, he seemed to know every single shark species, their scientific names, whom is thought to have begat whom evolutionarily, and he could instantly tell the ID of each tooth. Oh yeah, and remember how I said "Fate" had led me to want this trip at the exact same time that Mike announced that he was planning a trip? Yeah, well, he has gone on this trip almost every weekend since January.

Yeah - he's an enthusiast alright... Thanks Mike - you rock!

We awoke the next morning and headed for the dirty, trash-filled, broken glass-laden creek running near East Carolina University campus known as "Green's Mill Run." This place is famous for yielding big megalodons and great whites (and ancient soft drink bottles and bongs). The creek cuts through layers from the cretaceous to the pliocene, so things found in it can range from about 2.5 to 145 million years old!

The story was much the same at "GMR". I found quite a few great teeth (though I didn't feel as inclined to pick up every tiny tooth after the previous day), including another awesome Mako.

This was while I was still clean...

This was while I was still clean...

Mike found an AMAZING great white, and lot's of other great teeth - many of which he gave to me.

Mikes Great Whites - beautiful

Mike's Great Whites

I sat and watched an awesome freshwater eel hunting minnows in one beautifully sunny pool - a first for me. We didn't have freshwater eels in NW Arkansas (that I'm aware of).

Mike found and gave me what I easily consider the coolest fossil I now own (he already has several): the fossilized inner ear bone of a whale. What kind? not a clue.

Whales inner earbone

Whale's inner earbone

We visited one particular spot in the creek that cuts through this crazy shell layer filled with huge scallops and various mollusks.

Sea Scallop (as opposed to land scallop)

Fossil Sea Scallop (as opposed to land scallop)

Some sort of big bivalve - and WHOLE!

Some sort of big bivalve - whole and heavy!

By 6PM my back and arms would not let me sift a single more shovel load. Thus we called it a day.

Here's the total haul from Saturday:

The GMR Catch

The GMR Catch

What would have been HUGE megalodons, a very nice Mako, and a root-less great white

What would have been HUGE megalodons, a very nice Mako, and a rootless great white

The Makos and the White

The Makos and the White

The other shark teeth

The other shark teeth

Another cool fossil that exists by the millions in GMR is the belemnite. Belemnites were cephalopods related to modern cuttlefish. Only one part of it's body is normally fossilized: a calcite rod in it's body that assists in maintaining proper buoyancy. These things are just cool looking - orange and long and pointy, with a translucent character in the water.

Fossilized Belemnite guards (or rostrum)

Fossilized Belemnite guards (or rostrum)

And finally, the creek has quite a lot of pieces of whalebone:

Fossilized whale bone

Fossilized whale bone (and a cretaceous oyster - according to Mike)

All in all, this was by far the coolest natural history excursion I've been on (or perhaps second best behind a trip to Big Bend where I found an ammonite 4 feet in diameter - I left it there).  If you read this far - I hope you enjoyed my tale. If you didn't...well... you can't see this anyway.

The total weekend haul!

The total weekend haul!

Cat included for scale :)

Cat included for scale :)

Next up: fossil hunting in Pennsylvania in the next month or two! When exactly or where I don't know. But it will be fun!

2Jul/09Off

Grandpa’s Pet Therapod

nope - not a fake at all...

nope - not a fake at all...

I hang out online sometimes with a bunch of like-minded fossil-enthusiasts (The Fossil Forum).

Tonight somebody posted this:

Just watched the new this evening and they were talking about a dig going on right now outside of Glen Rose, on the McFall ranch. The news showed the footprints of the therapod and the human prints together. It was interesting. For report go to cbs11tv.com

So I mosied over to the Dallas, TX CBS news site and found the article "Local City Known As Dinosaur Capital Of Texas, by Arezow Doost."

Sounds innocuous enough for a title, right?  Then I read the first three sentences:

"Did you ever think that there were dinosaurs in North Texas?

As it turns out, this is one of the most prolific areas for dinosaur tracks in the state. One group of scientists have even found tracks dating back millions of years."

Read that last sentence again:

"One group of scientists have even found tracks dating back millions of years."

Cause, you know, all those other groups found tracks that weren't millions of years old...
(for those of you who missed out on elementary school, dinosaurs went extinct at the end of the Cretaceous sixty-five million years ago.)

Absolutely hilarious...and mind-numbingly maddening.

After reading a bit more, then you learn what it is really about:

"Scientists believe that one of the most unique findings is human prints dating back to the same period as the dinosaur prints. "We are looking for the truth," said Baugh. "We don't want anything else but the truth.""

I rolled my eyes. Obviously, I had a feeling what I would find out with a little search, but I decided to check out the scientist quoted in the piece, because I thought it was a bit odd that he said "We are looking for the truth. We don't want anything else but the truth."

You see, that is a very non-scientist thing to say in a media piece, and it instantly threw up a red flag to me. I say this because when one is actually in the practice of being a good scientist, a statement like that is like a commercial fisherman saying "no really, we're just out here to catch fish." What else would a fisherman be fishing in the ocean for? If you're a scientist, a statement like that is less than unnecessary.

Yeah this guy, Carl Baugh, is a young earth creationist discredited in the scientific community and with a questionable education. He is obviously seeking to prove his own wrong beliefs - not actually do what good scientists do, which is let the data speak for themselves. Check this out for some rather hilarious reading on Baugh: http://en.wikipedia.org/wiki/Carl_Baugh

Sigh...it is Texas after all (I was born and raised in east Texas, FYI)

As an added moronic bonus, if you look at the url of the story you'll see that it's filed under "pets."
(http://cbs11tv.com/pets/Texas.Dinosaur.Capital.2.1069336.html).

What kind of of idiots are running that station?

One thing about the fossil record - it's insanely consistent across both time and continental space, if fragmentary. And it has consistently shown us that human and therapod existence is quite a few tens of millions of years apart.

Hell, mammals were barely existent back then, compared to today. But primates? LOL - no.

***

Side note: I'm going fossil hunting in Aurora, NC tomorrow and at Greens Mill Run in Greenville, NC on Saturday!!  Shark teeth here I come. Please just let me find a megalodon.

26Jun/09Off

Echinodermata For The Win!!

I'm back!!!

Oh...you never realized I was gone?

Ah well, that's ok, because I AM back - back from a stressful few months of wondering where I would end up, how I would feed my babies (i.e. cats) and their baby-momma (my wife - yeah that does sound rather gross), and several dozen unknowns also thrown into the mix.

And after all the trials and tribulations, I can now state with certainty that I got the one job in my new future hometown (Pittsburgh) that I wanted more than anything: a post-doc in the lab of Dr. Veronica Hinman at Carnegie Mellon University.

What will I be doing you ask?

Well, I will be doing none other than studying the evolution of gene regulatory networks (GRNs). Specifically, I'll be looking at GRNs in the context of development using the wonderful sea critters in the phylum Echinodermata. For those of you not in the know, the "spiny-skinned" echinoderms are the asteroids (starfish/sea stars), ophiuroids (brittle stars), echinoids (sea urchins), holothuroids (sea cucumbers), and crinoids (feather stars, sea lillies and such).

Click for larger! Or Click HERE for super high resolution posters.

That's right folks - I am now at least an honorary marine biologist! ... kind of.  I don't know if the real marine biologists would ever deign to allow me such a title, but I can call myself whatever I want.

Many of you may know this already, but the process by which a single fertilized cell becomes a complex organism is an insanely intricate one. DNA is often called a "blueprint" for life, however in reality it's more like a cooking recipe informing each cell which ingredient to add and when, where, and how to add it - all codified into a multi-layered genetic computer program with kernels, plug-ins, sub-circuits, and all sorts of other technobabbly organic craziness.

This is where the "Gene Regulatory Network" comes in - the GRN is that central biological software controlling and allowing life itself. Not only will I be studying the structure of these networks in echinoderm development, I'll be looking at the evolutionary context of the echinoderm networks in relation to each other to suss out how they work and which parts of the networks are conserved (or not) between these amazing creatures that diverged from each other about 500 million years ago.

I'll initially be working on the "endomesoderm" network in the sea star, Asterina miniata. Down the line I'll also be contributing to the development of the sea cucumber as a new model for studying "evodevo".

In celebration, I spent a fair bit of time getting back to my art roots creating the above cladogram in the sand of the Echinoderm phylum (which you can get a poster of here if you're into echinoderms. I rendered it out in pretty high resolution, so you will definitely be getting a high quality poster. I'm pretty proud of it as it took quite a bit of work in the Blender program).

I spent a while trying to find time-lapses or animations of starfish development online, to no avail. Thus I spent a week of much needed downtime to create this computer animation: (note - you can also watch it in High Definition on youtube)

NOTE: The details of the actual metamorphosis of the rudiment into the juvenile are not accurate - it's quite hard to animate these types of changes - and to be honest I haven't actually seen these creatures in the flesh. But it's good enough to get a good idea of how the whole developmental process occurs in this type of sea star.

Anyway, I'm sure I will have much much more to say about the evolution and development of echinoderms in the future so I'll leave it at that for now.

Hopefully, I can at least be an honorary member of the cool kids club, the marine biologists: Kevin, Eric, Andrew, David, Miriam, Christie, Rick, Mark, Jason, Chris, and all the others I'm surely missing.