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.
"Only a handful have ever been found before. But none like her. Her name is Lyuba. A 1-month-old baby mammoth, she walked the tundra about 40,000 years ago and then died mysteriously. Discovered by a reindeer herder, she miraculously re-appeared on a riverbank in northwestern Siberia in 2007. She is the most perfectly preserved woolly mammoth ever discovered. And she has mesmerized the scientific world with her arrival - creating headlines across the globe. Everyone wants to know... how did she die? What can she tell us about life during the ice age and the Earth's changing climate? Will scientists be able to extract her DNA, and what secrets will it uncover?" - NGC
Waking the Baby Mammoth, a new program by the National Geographic Channel premiering Sunday, April 26th at 9PM, tells the tale of a single accidental discovery of a frozen baby mammoth in the Siberian tundra and how this discovery has enriched our understanding of these extinct magnificent beasts. (My quick review: 5 stars. watch it! it's beautiful and fascinating.)
However, this is not a standard paleontological nature show about mammoths in general or what life was like during the Pleistocene. Nor is this program purely about the science behind this bountiful discovery, though the arduous nature and reality of the scientific process is certainly one of the show's stars. In fact, one of the most fascinating aspects of this program is its focus on the one man and his strange culture (from an American perspective) that led to the discovery of one of the most important findings in mammoth biology. Waking the Baby Mammoth is as much an education on the hardy nature, harsh lifestyle, and animist beliefs of the reindeer herding Nemets nomads of Siberia as it is a show about the mammoth.
Without spilling too many details, the show begins with the incredibly fortuitous discovery of Lyuba, a 40,000 year old mammoth calf, by the nomadic Yuri Khudi (and his sons), a man whose animism dictates that disturbing the remains of the dead will lead to a curse. Too often with such paleontological findings as this, the preserved creature would be dug up and put on the market, leading to irreversible decomposition and the loss of a treasure trove of valuable information. However, Yuri had enough understanding and foresight to contact authorities in Russia, which began the intensive examination and retrieval of Lyuba (including a short drama during which Lyuba disappeared due to thievery). It is implied though not fully explained that Yuri had some inkling of what he had found - in fact he believed that the corpse had been put in his path for a reason, though he dared not disturb it himself.
The program subsequently follows a very well-done modern scientific storyline, detailing the scientific process and hurdles in understanding from whence Lyuba came, how she died, and what she can tell us about her Pleistocene life. That being said, apart from specific experiments involving high tech C-T scans, internal tissue extraction via some remarkable endoscopy, and dental examinations, the program does not delve overly deep into the intricate data. It's impossible to watch the work on Lyuba without feeling the anxiety the researchers must have felt in getting everything done right the first time on so precious a specimen.
From my own scientist perspective, I think the program goes as deep as it needed to portray the scientific importance of Lyuba's discovery. More importantly, the show succeeded best at precisely what it is intended to do: to bring drama and a deep emotional human connection to a quite amazing story. Throughout the program, we are presented with many truly stunning 3D animations of Lyuba and her mother. In cinematic form fitting with the story's message, Lyuba has been brought to life as an active furry baby mammoth tromping along next to researchers as they contemplate the frozen carcass' secrets. The visuals are beautiful, as the light shines off the baby's fur at just the right angles and her shadows dance in just the right way to really make her come alive - like a corporeal ghost watching her own ancient body bring her back to life in our own minds. Some of the more touching scenes involve Yuri himself near the end. A full year after his initial discovery, he was finally given the chance to suit up in aseptic surgical gear and join the researchers in the lab to witness first hand what his discovery meant to the rest of the world so foreign to him. It's hard to imagine what must have been going through this relatively "simple" man's mind, but his own expressions make it clear that he had come to understand the importance of his discovery and its impact as a blessing - not a curse - on our understanding of life's history. In his final farewell we see him and the animated Lyuba together in a quite touching cinematic juxtaposition of this nomadic reindeer herder and his now eternal connection to baby Lyuba.
Waking the Baby Mammoth is a tale that depicts the contrasting of cultures, worldviews, and personal beliefs of humanity amidst the backdrop of a seminal scientific discovery. Where this program succeeds remarkably well is in making the viewer understand the integral importance of these disparate cultures and the fortuitous convergence of good fortunes that allowed Lyuba to give us a new view of a lifeform long lost to us.
It is in this sense that NatGeo has truly woken the baby mammoth and placed her firmly within our modern human minds and hearts.
Christie over at Observations of a Nerd also has a glowing review up now.
Once again I'd like to thank Minjae Ormes (Digital PR Consultant for NatGeo) for 1) the opportunity to review the NGC programs and 2) for being so cool in our communications.
If your interested, also check out my recent review of NatGeo's Kingdom of the Blue Whale.
The National Geographic Press Release
A MAMMOTH SURPRISE.
NATIONAL GEOGRAPHIC CHANNEL'S WAKING THE BABY MAMMOTH FOLLOWS A GLOBAL FORENSIC INVESTIGATION INTO THE LIFE AND DEATH OF THE BEST-PRESERVED BABY MAMMOTH EVER DISCOVERED
Scientists Embark on a Paleo-Detective Expedition to Reveal the Secrets of this 40,000-Year-Old Phenomenon, as Centuries-Old Indigenous Culture Meets Modern-Day Science
"This baby looks like you could snap your fingers and she would wake up and walk."
Narrated by Award-Winning Actor Victor Garber,
Waking the Baby Mammoth Premieres Sunday, April 26, 2009 at 9 p.m. ET/PT
(WASHINGTON, D.C. - APRIL 1, 2009) Only a handful have ever been found before. But none like her. Her name is Lyuba. A 1-month-old baby mammoth, she walked the tundra about 40,000 years ago and then died mysteriously. Discovered by a reindeer herder, she miraculously re-appeared on a riverbank in northwestern Siberia in 2007. She is the most perfectly preserved woolly mammoth ever discovered. And she has mesmerized the scientific world with her arrival - creating headlines across the globe. Everyone wants to know ... how did she die? What can she tell us about life during the ice age and the Earth's changing climate? Will scientists be able to extract her DNA, and what secrets will it uncover?
Now, from behind the headlines, National Geographic Channel's (NGC) Waking the Baby Mammoth sets out around the world on a cutting-edge forensic investigation into Lyuba's life and death, 10,000 years after most populations of her species became extinct. Narrated by award-winning actor Victor Garber, the two-hour special premiering Sunday, April 26, 2009 at 9 p.m. ET/PT tells Lyuba's incredible story with insight from her indigenous Siberian rescuers and the scientific community so captivated by her, as a centuries-old nomadic tribe meets modern-day science in this fascinating cultural exchange. The discovery of this baby mammoth gives researchers their best chance yet to build a genetic map of a species that vanished at the end of the last ice age. Through her DNA, Lyuba could finally explain why the prehistoric giants were driven to extinction, share clues about their migrations, and perhaps shed light on climate change. Could she even some day help to resurrect mammoths? With research funded in part by the National Geographic Society, Lyuba's journey will also be the May cover story of National Geographic magazine.
Filmed on three continents, Waking the Baby Mammoth presents a 21st century paleo-detective expedition that takes viewers from the tundra of remote Siberia to cities in Japan, Europe and North America as we join a nomad and leading scientists to "awaken" this startlingly lifelike baby. We travel back to the ice age with Lyuba via CGI animation and then fast-forward to the present to reveal the latest innovations in woolly mammoth research, including advanced computed tomography (CT) scanning and DNA analysis, searching for clues to her species' life, extinction and scientific future.
Waking the Baby Mammoth first follows paleontologist Dan Fisher and mammoth "hunter" Bernard Buigues back to the spot where Lyuba was discovered in May 2007. She was found on a snowy riverbank by Yuri Khudi, a nomadic reindeer herder in Russia's remote arctic Yamal-Nenets region. Named after Yuri's wife, Lyuba was turned over to the scientists at the Salekhard Museum in Siberia, which is where the next chapter in her journey began.
The film next accompanies Lyuba to Japan's Jikei University School of Medicine, where her body undergoes three-dimensional computer mapping that produces detailed images of her internal organs and structure, providing scientists with insight into the possible cause of her death. With all but her tail and woolly coat of fur, the CT scans showed that the 200-pound baby was in excellent health when she died, with healthy fat tissue and no damage to her skeleton. The scientists conclude that Lyuba met her end by drowning or falling into deep mud, as there are large amounts of sediment packed into her trunk, mouth and trachea. They believe that her final muddy resting place became part of the region's permafrost, preventing decay and keeping her remarkably intact, down to her perfect trunk and largely unblemished skin.
Researchers have long debated whether woolly mammoths' extinction was due to climate change or overhunting by humans. Now they hope to compare her DNA with that of other mammoths from the ice age to trace the migrations of mammoth populations over time and help solve the mystery of her species' disappearance.
Finally we travel with Lyuba to the Zoological Institute in Saint Petersburg, Russia, to follow the scientists as they conduct an autopsy and analyze her tissue, bone and teeth to reveal insight into the structure of mammoth organs and muscles. Their study is able to confirm Lyuba's age, her diet, the season of her death and environmental conditions for her mammoth herd in Siberia during her short life. In fact, they are even able to extract pollen that remained in her lungs, which can be used to reconstruct prehistoric plants that grew on the site where Lyuba died. The bone and tissue samples that are collected will also be used for future DNA analysis and shared among mammoth research teams worldwide, so experts across the globe can learn from her.
For mammoth scientists, discoveries like this truly come once in a lifetime. As Alexei Tikhonov of the Russian Academy of Science says, "Lyuba is a creature straight out of a fairy tale. When you look at her, it's hard to understand how she could have stayed in such good condition for 40,000 years ... This is the most amazing discovery since we've been studying mammoths."
For more information on the best-preserved baby mammoth ever discovered, visit natgeotv.com/mammoth beginning in early April 2009.
Waking the Baby Mammoth is produced by Woollyworks, Inc. Producer is Adrienne Ciuffo and director is Pierre Stine. Special thanks to The International Mammoth Committee. For National Geographic Channel, executive producer is Chris Valentini; senior vice president of special programming is Michael Cascio and executive vice president of content is Steve Burns.
Based at the National Geographic Society headquarters in Washington, D.C., the National Geographic Channel (NGC) is a joint venture between National Geographic Ventures (NGV) and Fox Cable Networks (FCN). Since launching in January 2001, NGC initially earned some of the fastest distribution growth in the history of cable and more recently the fastest ratings growth in television. The network celebrated its fifth anniversary January 2006 with the launch of NGC HD which provides the spectacular imagery that National Geographic is known for in stunning high-definition. NGC has carriage with all of the nation's major cable and satellite television providers, making it currently available to nearly 70 million homes. For more information, please visit www.natgeotv.com.
Russell Howard, National Geographic Channel, 202-912-6652, RHoward@natgeochannel.com
Chris Albert, National Geographic Channel, 202-912-6526, CAlbert@natgeochannel.com
National Broadcast: Dara Klatt, 202-912-6720, Dara.Klatt@natgeochannel.com
National & Local Radio: Johanna Ramos Boyer, 703-646-5137, Johanna@jrbcomm.com
National Print: Christie Parell, The Fratelli Group, 202-822-9491, CParell@fratelli.com
Local Print: Licet Ariza, The Fratelli Group, 202-496-2126, LAriza@fratelli.com
Digital: Minjae Ormes, Independent Digital Consultant, 917-539-7646, Minjae.firstname.lastname@example.org
Photos: Christine Elasigue, National Geographic Channel, 202-912-6708, email@example.com
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).
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?
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.
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.
- 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.
- William C. Aird. Endothelial biomedicine. Edition: illustrated. Published by Cambridge University Press, 2007
- 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
- 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
- Top image © Dr Julian Gutt and Alfred Wegener Institute
- Icefish larval image by Uwe Kils
Previous Adaptations of the Week:
I am a fossil collector.
Ever since I was a small child I have been collecting fossils. In fact, I can trace my own fascination with biology directly to my discovery that the very house in which I lived (actually a trailer back then), was set upon land literally made of these long dead and formerly ocean-dwelling ancestors and distant cousins. I'll never forget the awe that crept into my little brain as I tried to imagine enormous oceans covering my forested Ozark mountains.
When I was very young, my Mamaw (paternal grandmother) gave me a simple large toolbox for Christmas - a toolbox with a myriad little compartments intended for the sole purpose of housing my growing "rock collection."
For years I filled this box and a couple more with fossils, rocks, gems, shed snake skins, feathers, arrowheads, seashells, and all manner of relatively non-decomposable animal and plant remains - almost all of which I found myself.
The time came when I was not content to let my collection sit in toolboxes in a closet. Thus I built a shadowbox coffee table during graduate school (with super thick glass so my cats could leap onto it from 10 feet away without smashing my fossils...er...the glass and themselves). Now my collection fills my coffee table and almost every bookshelf in my home.
I've amassed a decent collection - I'm proud of it anyway, though any paleontologist or geologist would almost certainly laugh at it. Most of them are simple ocean invertebrates, as most of them came from Carboniferous Period limestone of the Ozark Mountains (the entire region is pretty much made of pure crinoids).
All of the above being said, I'm a bit ashamed to admit that I don't know that much about many of my fossils.
Thus, I am starting this series of posts to catalog my entire collection and to see what the experts out there can teach me and all of us about some of our long lost branches of life. Please, if you can add any information whatsoever, it would be much appreciated - i.e. taxonomy, factoids, comments, conjecture, anything. And please point out if I have identified anything incorrectly - a very real possibility.
For this first installment, I am going to begin with my most recent additions - all found this weekend in Bella Vista, Arkansas where I returned for my mom's wedding.
A hat tip goes out to my four nieces (ages 9 to 12) for helping me find them.
Location: Bella Vista, Benton County, Arkansas
What I know: based on my limited understanding of the region's geology, these rocks are primarily limestone from the carboniferous period (and I believe they are towards the boundary between Pennsylvanian and Mississippian - but I could easily be wrong. I know very very little about geology).
Note: You can click on all images for higher res/quality images. These are highly compressed for bandwidth. I've tried to give multiple views of each fossil.
#1 - Crinoid
#2 - Productid Brachiopod - Order Strophomenida
Update: information provided by Chris Nedin, of Ediacaran: "looks like a productid brachiopod. Order Strophomenida, Suborder Productidina. They can be distinguished by being large, very rounded, with a thick, heavy shell, and along the top, a very straight hinge line, with almost nothing appearing above the hinge line. An example is here at image 408."
#3 - Spirifid Brachiopod - Order Spiriferida
Update: information provided by Chris Nedin, of Ediacaran: "an internal mold of a spirifid brachiopod, Spiriferida, Suborder Spirifieridina. The shell has been filled with sediment and that has hardened. Then the original shell has dissolved away, leaving the sediment inside, which is what you see. The shape is caused because the shell tapers down to a point away from the centre, and curls somewhat. An example is here."
#4 - Rhynchonellid Brachiopod
#5 - Spirifid Brachiopod
#6 - Crinoid
#7 - Possible Spirifid Brachiopod
#8 - Shelly strata
I know - these aren't exactly impressive specimens. However, I already had them unpacked and laid out so I figured I'd start with these. I definitely have some other cool ones to come in future posts.
If you know of any fossil aficionados, please send them this way, as I would really like to know at least a little bit more about my collection. If any of you end up being particular helpful, I may just send you one of my awesome limestone rocks made of pure crinoid discs (they're much cooler than those above), assuming you don't already have some or consider them too bland