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!

25Mar/09Off

Adaptation of the Week – Channichthyidae Icefish Blood and Antifreeze

I owe the following example of evolutionary adaptation to the always amazing evolutionary and developmental biologist Dr. Sean B. Carroll, from his lecture "Making of the Fittest" for the Darwin College - Darwin Lecture Series, available at iTunes U (I highly recommend everyone give it a listen).

The Red Blood Cell-less Icefish © Dr Julian Gutt and Alfred Wegener Institute

The Red Blood Cell-less Icefish © Dr Julian Gutt and Alfred Wegener Institute

Imagine that you are a fish - exothermic and thus unable to regulate your own body temperature - and the contingent foibles of natural history have all conspired to leave you and your kind in the frigid oceans of the Antarctic just as they are beginning to reach the freezing point (10-14 million years ago).

You like the cold and are well adapted for it, but these temperatures are beginning to give even you - a master of the cold - the icthy chills.

Now imagine that the hands of mother nature have given you the tools to change your own genetic code, and thus your nature, allowing you to make yourself even more suited for waters that are 2 degrees celsius below the freezing point of pure water.

What would you do? Would you inject your DNA with a molecular antifreeze? That seems like a reasonable addition - one we will get to momentarily.

But if you were a genius of bioengineering would you reach out a molecular scalpel and hack away the genes that allow the production of red blood cells, hemoglobin, and myoglobin, leaving only molecular fossils behind?

Icefish Larva

Icefish Larva © Uwe Kils

It doesn't seem like a particularly well thought out plan. But then again, neither you, the fish, nor mother nature are genius bioengineers. Fortunately for life, the forces of evolution still manage to get the job done, however sloppy the end results (yes, technically the job is never done - forgive my metaphor wearing thin).

In fact, natural selection performed just such a feat somewhere around 8.5 million years ago in the ancestors of a flock of related species in the Antarctic: the Channichthyidae icefishes (also known as crocodile icefishes or white-blooded fishes).

As we all know, liquids tend to become more viscous in the cold. Just compare maple syrup before and after refrigeration. Blood viscosity would have no doubt been an issue in the ancient ice fish ancestors, or at least one that could be improved upon. Normal vertebrate blood is filled with big, round, and red blood cells coursing through the blood vessels. Now imagine lowering the temperature of the blood below the normal freezing point of water - that's bound to create some significant resistance.

But aren't erythrocytes critical for carrying oxygen? How could an organism just dispense with them completely? As many scientists know, one of the great things about really cold water is that it can be packed with oxygen. Such is the case with the waters of the Southern Ocean, which are saturated with oxygen.

Thus, it seems that at some point, the icefish ancestors developed mutations in the pathways that result in red blood cell production. Furthermore, the species eventually acquired a deletion in the key genes of red blood cells: the alpha and beta hemoglobin genes. No longer could this fish produce hemoglobin.

As is often the case with evolution through loss of gene function, the deletion wasn't perfect. Almost all vertebrates have both hemoglobin genes lying next to each other within the genome. In most Channichthyidae icefishes, the beta hemoglobin gene has been completely deleted, along with all but the truncated end of the alpha hemoglobin gene (interestingly, these fish have lost their myoglobin gene as well)1. To quote the original paper by Near et al.:

"Despite the costs associated with loss of hemoglobin and myoglobin in icefishes, the chronically cold and oxygen-saturated waters of the Southern Ocean provided an environment in which vertebrate species could flourish without oxygen-binding proteins."

The upshot of all this is that the icefish has completely clear blood lacking in any erythrocytes - and they are the only species of vertebrates to have such a trait.

Normal 2 globin genes vs. lost icefish globins - modified from Near et al 2006

Normal two hemoglobin genes vs. lost icefish hemoglobins - cropped figure from Near et al 2006

Of course, a few other supporting traits evolved as well. Their hearts are significantly larger than other fish hearts, and they pump 4 to 5 times larger volume of blood per stroke2. Their capillary beds have become much more dense as well to make sure all their tissues get adequate oxygenation. Of course, like amphibians that breathe through their skin, with the loss of red blood cells, those that were better able to absorb oxygen tended to outperform their cohorts. Thus they became scaleless as well.

As if these adaptive feats weren't cool enough (pun intended), the antarctic icefishes have evolved their own antifreeze as well3,4. What's amazing about this antifreeze (an Antifreeze Glycoprotein - or "AFGP") is that it represents one clear cut case in which a gene with a specific function has evolved into a separate gene used for a completely different function in a novel way. In the case of the icefish, the ancestral gene was a trypsinogen (a pancreatic digestive enzyme), which has been mutated and co-opted to be secreted and distributed throughout the body to act as an antifreeze. Specifically (for you biologists out there), the 5' secretory signal and 3' UTR sequences of trypsinogen were tacked onto an amplified nine nucleotide sequence from within the trypsinogen precursor to create the novel antifreeze peptide.

So here we have in the icefish's adaptation to the cold, at least one case of de novo creation of a novel gene with a new function from an old gene, as well as the loss of two other genes that have left genomic fossils behind to whither in the weathers of time.

It may not be the cleanest or best engineered solution to the problem of living in an Antarctic Hell (or perhaps Heaven from the perspective of the fish), but this messiness of evolution is precisely what makes it so incredibly beautiful.

References

  1. Near T.J., Parker S.K.,  Detrich H.W. A genomic fossil reveals key steps in hemoglobin loss by the Antarctic icefishes. Molecular Biology and Evolution, v.23, 2006, p. 2008 - 2016.
  2. William C. Aird. Endothelial biomedicine. Edition: illustrated. Published by Cambridge University Press, 2007
  3. Chen L., DeVries A.L., Cheng C-H. C. Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid?fish. PNAS, April 15, 1997 vol. 94 no. 8 3811-3816
  4. Chen L., DeVries A.L., Cheng C-H. C. Convergent evolution of antifreeze glycoproteins in Antarctic notothenioid fish and Arctic?cod. PNAS, April 15, 1997 vol. 94 no. 8 3817-3822
  5. Top image © Dr Julian Gutt and Alfred Wegener Institute
  6. Icefish larval image by Uwe Kils

Previous Adaptations of the Week:

  1. Timber Rattlesnake Camoflage
  2. The Aye-Aye’s Freaky Finger (I’ve Been Cursed by an Aye-Aye!)
  3. Flatfish Eyes & Recapitulation Theory
  4. Bird/Crocodile Symbiosis?
  5. Insect Dorsal Ocelli
12Mar/09Off

What would YOU like to know about sharks?

Why do sharks matter?

Why do sharks matter?

One of my science blogger buddies, WhySharksMatter over at Southern Fried Science, has received the opportunity to interview an influential shark researcher, Dr. Dan Abel. He is asking for anyone and everyone to pose a question you would like asked of Dr. Abel. Perhaps you want to know something about sharks or maybe something about what it's like to study sharks or why he chose to study them. There are any number of fascinating things to be asked. I asked an interesting one myself (at least I think it's interesting).

So if you have any shark-related questions you'd like answered by an actual shark expert, head over to this post right now and leave your question in the comments section.