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


Nature Walk #2 – Birds and a Burger

For my next Nature Walk, on my Friday lunch break I decided to take a quick stroll around the lake at the NIEHS campus, camera in hand. Over the past couple of month several coworkers have spotted two river otters in the lake (which is strange indeed). I even managed to spot one while staring out the cafeteria window.

Unfortunately, I did not see the otters, though I will most certainly be attempting to capture them on digital film next week... I did see the following... (FYI: I am not an experienced birder - if I misidentify, feel free to let me know. Also: these are highly compressed images to limit bandwidth - click for higher res).

Beautiful lake between the NIEHS and EPA campuses

Beautiful lake between the NIEHS and EPA campuses

First up, a flock of ruddy ducks (Oxyura jamaicensis):

Ruddy Ducks


Ruddy Duck

so my tail's stiff...what of it?

Ruddy Duck

Get back to work...

And of course, our ubiquitous Canada Goose (Branta canadensis). We literally have hundreds of these birds all over campus year round, covering every surface with green refuse. I look forward to nesting season when they develop severe huffy attitudes that involve a lot of loud hissing (but they're really all talk).

A while back they hired a company to capture most of them and relocate them...yeah...that didn't work (too many geese leads to many problems, environmental and otherwise).

Bring it on Cobra Kai

Bring it on Cobra Kai

Walk on by...

Walk on by...

And the less exotic, but still wonderful American Robin (Turdus migratorius) far away and HIGH up in a tree (I was surprised this photo even turned out at all.


Fluffed in the wind

After my walk around the lake, I went for a burger at Wendy's (I know - horrible - but they're so tasty). All of the following were taken from my car in the parking lot and at my parked eating spot.

Every year about this time, a huge flock of Ring-Billed Gulls (Larus delawarensis) shows up in this fast-food district. You coastal folks may bore of them, but we are pretty far inland, and I grew up in landlocked Arkansas, so I still find gulls utterly fascinating.

Loves me some burgers

Give me fries!!

Call me Narcissus...

Call me Narcissus...

Beautiful eyes.

Beautiful Eyes (mature vs. immature)

One sad bird had a severely gimpy foot. But it seemed to be surviving...thanks to fast-food throw aways. I must say that it looked to be in some pain walking.

Victim of a fisherman

Victim of a fisherman (tangled line and rig)

And finally, I retreated to my favorite natural spot to eat, parked near a tiny copse of pines. Despite the fact that I always pay attention to nature, I somehow had never managed to see the following bird. I could tell it looked like a nuthatch - I'm very familiar with the White-Breasted Nuthatch (Sitta carolinensis) as we had hundreds on my property in Arkansas - but I had no clue what it was and had to look it up when I got home.

It's a Brown-Headed Nuthatch (Sitta pusilla). He was pretty cute - he would look in the hole and poke around, then jerk his head around to make sure no one was watching, then do it again and again.

Paranoid much?

The Paranoid Nuthatch

The Brown-Headed Nuthatch in action...

Shortly thereafter it was back to the lab...

Previous Nature Walks:


Tagged by Rick MacPherson’s Google Meme

Okay, my excuse is that I have yet to participate in a "meme" yet (despite being tagged by several).

The infamous Rick MacPherson of Malaria, Bedbugs, Sea Lice & Sunsets came up with his own little game wherein he determined a set of search terms that would result in his own blog ranking as the top hit (such as "coral reefs, conservation, queer" and "zelnio, conservation, blog, coral, drunk").

The exercise ended up being more entertaining than I anticipated. My goal was to find the most entertaining or impressive search terms.

In no particular order, here are some search terms that will give you Biochemical Soul as the #1 Google search hit (no quotes or advanced googling were used):

  • andrew kevin dueling penises (that explains some of my traffic - it's totally invertebrate biology-related - I swear)
  • miriam oyster orgies (also invertebrate biology-related)
  • magnum p.i. blue whale
  • daniel darwin beard
  • timber rattlesnake camouflage
  • flatfish eye adaptation
  • aye-aye finger adaptation
  • spaghetti monster animation
  • heron catfish video
  • daniel d brown ("daniel brown" doesn't pull this blog until results page 2)

Interestingly, I almost capture the the entire history of heart evolution - pretty sweet:

  • worm heart evolution (2nd behind a "pet heart-worm" site)
  • fly heart evolution
  • fish heart evolution
  • frog heart evolution
  • reptile heart evolution
  • bird heart evolution (#2 search result)
  • mammal heart evolution
  • human heart evolution (page 2 of results)

How about it Christie, Kevin, Allie, DNLee, Glendon? Care to give it a go?


Kingdom of the Blue Whale! – National Geographic

Heart the size of a Mini Cooper.
Mouth big enough to hold 100 people.
Longer than a basketball court.
Weighing as much as 25 large elephants.
It is the largest creature ever to inhabit the earth.
But we know precious little about it.

Kingdom of the Blue Whale - National Geographic Channel

Kingdom of the Blue Whale - National Geographic Channel

Yes, I am now an advertising pawn of big media. But it's a particular medium that I have no problem advertising for (and it will soon be obvious why). Thanks to the National Geographic Channel’s awesome Digital Consultant, Minjae Ormes, today I received an early screener DVD of their new TV program "Kingdom of the Blue Whale," which premieres Sunday, March 8, at 8 p.m. ET/PT.

Shiny Happy DVD (and press release)

Shiny Happy DVD (and press release)

Recently, Christie at Observations of a Nerd reviewed an early copy of NGC's Darwin Specials. She had a minor problem with one aspect of it, which I then expounded upon. I saw the problem as a critical one in which they incorrectly spoke about the mechanisms of evolution. I should note that having watched "Morphed" the rest of program's quality more than made up for my criticisms. Nonetheless, I told NGC's Digital Consultant that I felt a little bad criticizing it, but that I felt I had to. She replied thusly:

"Given your experience and expertise, I wouldn't expect anything less. I think it is precisely your personal take on the programs that would more likely convince other people to watch the programs via word-of-mouth, so I always appreciate an honest and thorough review."

It is for this open attitude that I have no problem reviewing NGC's programs and advertising for them. After all, who doesn't love the National Geographic Channel in general? This blog is all about science outreach - and that's what I see these NGC programs as being all about (other than the whole money thing).

This review is a tag-team collaborative review between myself, the aforementioned Christie at Observations of a Nerd, and Allie Wilkinson of Oh, For The Love Of Science! (link will be updated once their reviews are posted). Christie is actually a marine biologist, and knows a ton about whales, so she will focus on the science aspect of the program, while Allie is a conservation buff, and will cover it from that angle. I on the other hand, know a little more than your average non-scientist Joe about cetaceans and conservation, but infinitely less than Christie and Allie, so I will mainly give my impressions of the presentation, visuals, cinematography, etc., though there will no doubt be overlap.

Kingdom of the Blue Whale

“Our oceans once churned with giants, diving deep through liquid space. Today they’re few...and fragile”

The above quote is the opening line, delivered by the smooth yet husky voice of none other than walrus-mustachioed Magnum P.I. Tom Selleck. First off, let me say that Tom Selleck makes a really great narrator - smooth and never overly melodramatic.

For those of you who don't want to read the whole review, here is all you need to know: Kingdom of the Blue Whale is stunning! It's beautiful. It's sad. It pisses you off. Then it wows you some more. Then it saddens you again. Then it's uplifts you and then leaves you thinking "we've got to save them!"

The roller coaster of emotions is most assuredly intended exactly as such, for the program involves more than one story, though it does have a singular narrative at its center.

The central story involves one that perhaps many non-marine biologists and non-scientists may find shocking: despite the fact that the blue whale is the largest animal ever to have existed on the Earth, we had never seen them mating, we had never seen an infant, and we didn't even know where the blue whale goes to get it on and have babies. In fact, the smallest blue whale calves we've seen were about 40 feet long! To quote the program:

“Their calls travel hundreds of miles…but we can barely hear them.”

“They eat thousands of pounds of food every day…but we don’t know how they find it”

These are some of the many questions that several different groups of researchers set out to answer in the film. One of the things I loved about it is that each scientific question - including the nitty gritty details of how and where lab experiments were done, how samples were obtained, who is doing the research - was cut and intermingled in between the main story arc which took place almost solely on the open ocean.

It was clearly edited in a way to best bring the details of science to the attention-deficit American audience. First woo you in with stunning imagery and a tale of high seas adventure (and the constant question: "will they find a baby blue?"), then feed you a little bit of the behind-closed-doors labor of science - studies of the inner ear, communication, some genetics, illegal hunting - followed by more of the story arc, and so on.

Tagging the Blue Whale

Tagging the Blue Whale

The one tiny potential problem is that it is fairly long (1hr 36min without commercials) with a lot of research talk, such as in a segment on a portable genetics lab in a Japanese hotel looking for blue whale meat from a meat market. But I must stress that this is NOT a problem with the program per se, but a problem with today's viewing audience. In fact, I am incredibly pleased that they included so many different scientific issues. In the end, I enjoyed every minute of it, and would recommend that everyone watch it.

As for the visuals, what can I say, but "wow!" The videography in this program is amazing. Especially when you consider how few blue whales exist in our enormous oceans. Most of the awesomeness can simply be attributed to the inherent magnificence of the whales themselves, but the filming crew definitely deserves mad props. The opening scene sets the pace with a great close up of a blue whale's fully expanded pleated throat gathering up krill. After watching shots such as these, one can't help but want much more - more than is actually available. The scarcity of underwater close-ups is made painstakingly clear simply by watching how these beasts live, where they're found, and the difficulty just in studying them.

The logistical hurdles of filming and studying these animals was portrayed wonderfully. Keep in mind that an adult female can weigh up to 200 tons! And the researchers can only study the whales in tiny boats - it's simply too dangerous to attempt it from the large base ship. They have to constantly maneuver to stay behind the tail and anticipate their movements. Luckily, the whales were completely unspooked by tagging and tissue sampling. It was almost funny watching them try to attach suction probes to study their movement and sounds. To do this, they had to match the whales' speed in a (relatively) tiny outboard boat. On other days they had to battle storms, which made it completely impossible to spot the whales' “blows”.



The program was filled with beautiful shots of whales from high above, whales from the surface, and even from below them. My favorite involved the "CritterCam" that was placed by suction cup on one whale. You could see the whale's nose aiming upward toward the surface - then a dark cloud became visible - krill! - the whale opened it's gaping maw and swallowed the entire mass.

The transitions were quite well done, with several excellent computer animated sequences. These sequences were few and not done to make the program flashy. All of the animated sequences were used to illustrate important points, such as one beautiful animation of the earth overlayed with migration routes and sea floor topography, which gave me a great sense of the immensity of the ocean and the whales' habitat. Another cool animation showed water, temperature, and nutrient flow to illustrate the core habitat the researchers were searching for: the "dome," a tropical area with specific temperature layers that serve as a prime "nursery" for many ocean species. Or to put it more accurately, "an upwelling of cold, nutrient-rich water generated by a meeting of winds and currents west of Central America".

And then there was my favorite animation: a sequence showing a whale fetus in the womb.

The program was not completely without laughs - especially when Tom mentioned that a nine-month pregnant female carries a fetus that's 18 feet long. It just sounds so ridiculous! Or when the collection of a single sample of whale feces is described as a "tremendous triumph."

In the end, like pretty much every nature documentary these days, it's impossible not to leave with a sense of sadness and dread. A feeling that no matter how much programs like this help, no matter how many conservation movements take up the cause, the blue whale as we know it may be ultimately doomed. But hope is certainly not lost. Some populations may be making a slow comeback. Only time will tell.

I have a ton of notes that I'm leaving out, but I'm certain that Christie will spill much more than I. Don't worry - there is still much cetacean goodness that I haven't given away (hybrids between blues and fins?).

I'll simply leave you with the following questions:

Will they find the blue whale mating grounds?

Will they discover if the blues feed during winter unlike most whales?

Will they find the elusive baby blue whale?

Hint: the "money shot" is incredibly breathtaking.

Stayed tuned next month when we will be reviewing the other NGC program you can see on the above press release: "Waking the Baby Mammoth."

And for those of you wanting even more information on these great beasts, the official press release is below.



Scientists Unravel Mysteries of Critically Endangered Blue Whales,

and National Geographic is the First to Film an Infant Calf Underwater

Narrated by Emmy Award-Winning Actor Tom Selleck,

Kingdom of the Blue Whale Premieres Sunday, March 8, at 8 p.m. ET/PT

(WASHINGTON, D.C. - FEBRUARY 18, 2009) They are the largest creatures ever to live on our planet - larger than any of the great dinosaurs - yet few people have seen one.  They are one of the loudest animals on land or sea - capable of making sounds equivalent to those of a jet engine - but we struggle to hear them.  They deliver the world's largest babies, but despite their immense size, most of the places where the great blue whales calve their young have been among the world's greatest mysteries.

Blue whales are so rare that even experts know little about them, but we do know their future is threatened.  Blue whales in the Eastern North Pacific once numbered close to 10,000, but more than a century of whaling took its toll.  Even though the hunting of blues has been banned since the 1960s, today only about 2,000 are left in what is thought to be the largest known population on earth.  In an effort to learn more about these behemoths and help to protect them, an international team of scientists supported by the National Geographic Society sets out on an expedition to unlock the secrets of the blue whale and investigate why more are dying than at any time since the era of whaling.

Narrated by Emmy award-winning actor Tom Selleck, on Sunday, March 8, 2009, at 8 p.m. ET/PT, National Geographic Channel's (NGC) Kingdom of the Blue Whale takes viewers on a journey with some of the world's preeminent experts to explore the little-known wintering grounds of these elusive gentle giants, chart their migratory paths and identify where this population produces their young - vital information if they are to be protected.  The team even hopes they will be the first ever to film an infant calf underwater.  National Geographic Magazine will also have coverage of this landmark expedition in its March 2009 issue.

Filmed during sea voyages off the coasts of California and Costa Rica, Kingdom of the Blue Whale follows a watery trail of clues over hundreds of nautical miles, as scientists unravel answers to ancient mysteries hidden in the darkest depths of the oceans.  Back closer to shore, we investigate the traumatic deaths of four blue whales in one season - far greater than the one expected every few years.  Is man to blame, and what can be done to prevent the loss of additional whales?

Stunning HD underwater cinematography, CGI of the developing whale fetus, satellite imaging and insight from experts all help tell this new chapter in the story of the blue whale.  Using National Geographic's cutting-edge Crittercam®, an integrated video-camcorder and data-logging system that attaches to the whale's back with suction, this special also features the exclusive footage of the blue whale gulping krill - from the whale's perspective.

Aboard Oregon State University's research vessel the Pacific Storm, scientists use state-of-the-art equipment to find, study and listen to the Eastern North Pacific blue whale population.  Beginning in California, Dr. Bruce Mate, director of the Marine Mammal Institute at Oregon State University, places satellite tags on individual blues to track their location anywhere in the sea and collects skin samples to determine the sex of the whales.  Simultaneously, John Calambokidis of Cascadia Research in Olympia, WA, uses a camera to photo-ID blues and a crossbow to collect small skin samples for further study.

Employing a different type of tag, Dr. Erin Oleson, formerly of the Scripps Institute of Oceanography near San Diego, CA, decodes the whales' sounds - and what they might mean - by comparing the acoustic signals to the behavior they exhibit.  To their delight, the scientists are able to tag 15 blues.  But sadly, the team also comes across several dead blues off the coast of Santa Barbara, leaving the scientists distressed and elevating the urgency to find what is killing them.

Armed with technology and driven to solve the mysteries of these giants, the scientists next journey hundreds of miles through remote and dangerous seas searching for the wintering ground of these leviathans in the vast Costa Rica Dome, an area of the Pacific Ocean where cold water from the deep rises to just below the warm, tropical surface - an ideal blue whale habitat.  There the team faces the real challenge of finding and observing blues, which spend virtually all of their lives underwater and surface for only seconds at a time to fill their closet-sized lungs before diving again.

The team locates the whales in almost 1,000 square miles of remote ocean rarely visited by humans, and succeeds in their bold mission to confirm three whale behaviors never witnessed before at the Costa Rica Dome - courtship, calving and winter feeding.  By learning more about this secret spot, they win a huge victory toward protecting the creatures and their most vital habitat.  The team also confirms that calves are born at the Dome by documenting a mother blue whale traveling with an infant calf, the youngest ever photographed underwater and one of the rarest sights in nature.  And they confirm that blues feed all year round in this location - a behavior never before observed here.  Prior to this discovery, scientists had suspected that blue whales fed here during the winter months, but were never able to conclusively prove it.  In addition, the team verifies that blue whales interact with one another by singing, a behavior previously exhibited only by single males swimming alone.

Kingdom of the Blue Whale also opens a window into why these animals have become one of the most endangered species on earth.  Today, our oceans are busier and noisier, and resources the whales depend on are disappearing.  And while blue whale hunting is now illegal, they remain under assault by another killer - huge oceangoing cargo vessels that power through the sea day and night.  Blues have been known to become victims of ship strikes on occasion, but the numbers of fatalities have increased in recent years.  In fact, the four dead blue whales found during the making of this film were apparently killed by ship strikes.  Whale experts are exploring whether the amount of industrial noise in today's oceans might be a cause of confusion for blue whales, which can play a role in their tragic, but avoidable, deaths.

Join the National Geographic Channel as it unravels the web of mystery surrounding the elusive behemoths of the sea and uncovers the keys to the blue kingdom and its future.  As we witness the vitality of the whale's most critical behaviors, we now understand the complete life cycle of big blues and where science can concentrate its efforts to protect them.  As whale expert Steve Palumbi says, "It's probably harder to be a whale like that than it's ever, ever been before ... I think we have the power to protect them and let them have that chance."  To give them that chance, we must protect our seas over the years and decades to come ... for baby blue and for ourselves.

For more information on blue whales, visit


The Great Darwin Beard Challenge – Week 2

This week's installment of the Great Darwin Beard Challenge is live over at Southern Fried Science. We are in week two now, our sandpaper faces replaced by millimeter stubble.

It seems a long way from here to our bushy-bearded Darwinian goals. The "contest" will end on October 1st, the 150th anniversary of the inside cover date of the 1st edition of The Origin of Species - we began on Darwin's 200th birthday, February 12th.

Tiring of simple photographs of our burgeoning bearded faces, Andrew instituted a theme of "hats" this week. Apparently in the Southern Fried Science world, "enormous fake afro" is synonymous with "hat."

What will next weeks theme be?  Who knows. Give us some ideas.

We will be rotating through the blogs of Deep Sea News, Southern Fried Science, and here - so be sure to visit all three weekly :)

Great Darwin Beard Challenge History:


Adaptation of the Week – Flatfish Eyes & Recapitulation Theory

Most biologists at one time or another in their training have learned of the 19th century theory expounded upon by Ernst Haeckel called "Recapitulation Theory".

The theory's thesis: "Ontogeny recapitulates phylogeny." Don't worry - it's not as complicated as the biological jargon might imply.

Ernst Haeckels Drawings (1892 Romane copy)

Ernst Haeckel's Drawings (1892 Romane copy). Note: Haeckel oversimplified these drawings. I use them here as a simple illustration of the concept of developmental similarity.

The idea boils down to a simple one - one that seemed to make sense in light of the fact that the science of developmental biology had only just begun from a systematic standpoint. The idea: if you watch an organism develop from an embryo to an adult, you can watch it slowly move through the evolutionary steps that had created it. That is: development repeats evolution.

So a human embryo would first look like a fish, then a reptile, then a mammal, and finally a human. Of course, we now know that in a literal sense, the theory is completely and utterly wrong. No stage of human development, or of any other organism, correlates with a discrete step in evolution.

We are never fish. (Though we do have embryonic tails).

However, that doesn't mean that there aren't kernels of truth to the idea, if applied loosely. Take the most famous and classic example: embryonic human gills. You may have heard yourself that humans have gills as embryos. Unfortunately this claim arises from misconception and incomplete understanding of developmental biology. Humans do not - ever - have gills. But as embryos we do have "pharyngeal arches." These are little bumps around what you might consider the neck area of a developing embryo (see Haeckel's drawings above). And these little mounds of tissue do in fact remarkably resemble similar mounds found in fish - mounds that in fish develop into gills (Note: Haeckel vastly oversimplified these drawings. I use them here as a simple illustration of the concept of developmental similarity. See: Thanks Bjørn!).

One of the amazing aspects of developmental biology that much of the public does not generally understand is that evolution does not occur by adding new organs, appendages, or tissues to adult animals (whether through gradual steps or not). Evolution works by slowly sculpting the early embryonic clay of an organism.

Fish evolved these gill pouches as embryos - pouches that could then be sculpted into gills. As evolution waltzed and hopped along at its geological pace, genetic mutations began to change how these little mounds were sculpted, such that now in humans, these arches are sculpted into various parts of the face and head. A genetic program was already in place to control the shaping of the pouch. All that natural selection did was slightly tweak that program. For example, instead of a group of cells moving one direction, they moved another. Instead of becoming blood vessel cells, they became cartilage or bone cells.

Thus, while we now understand that we are not witnessing evolution in miniature during development, we are seeing pieces of our evolutionary history - little remnants that remind us of our relationships to our ancestors and also help inform us on what morphogenetic processes underlie evolution.

Which brings us to our adaptation of the week: the freaky asymmetric eyes of the flatfish.

Flatfish (

Flatfish (

Most people have probably seen a flounder - one member of the flatfishes. They have adapted to lie amongst the silty ocean bottom, hidden from predators and prey, flat on their sides. For a normal fish this might be maladaptive - they would constantly have one eye buried in the sand. Of course the negative of being one-eyed might be offset by being much more camouflaged and undetectable.

Luckily for the flounder, the eye that should be buried in the sand has moved around its forehead so that both eyes are on one side.

The flatfish eye served as one line of attack against natural selection back in the day - and Darwin himself didn't quite know how to answer the charges. Evolutionary gradualism would predict that through successive steps, the eye slowly moved upward toward the forehead and eventually to the other side of the face. But what advantage could a slightly moved eye give, if it still was on the wrong side? Alternatively, as Richard Goldschmidt postulated in the 1930s and 40s, perhaps a single monstrous freakfish was born with both eyes on one side, and this allowed it to lie flat without losing half its vision. It could have then survived and had lots of little freak fish babies of its own.

So how did the flatfish become the strange creature it is now? Let's first look at the developmental biology of the flatfish eye.

WANDERING EYES from Science News on Vimeo.

FROM FRY TO FISH from Science News on Vimeo.

Flatfish Metamorphosis

Flatfish Metamorphosis (Schreiber 2006)

It's been know for quite some time that flatfish larvae look like perfectly normal, symmetrical, and upright fish. The picture to the right is from a study by Alexander Schreiber in the Journal of Experimental Biology from 2006. As you can see, at early stages the larvae are normal, but progressively tilt and become horizontal as one eye moves across the face. He also showed in this study that eye movement and flattening behavior occur independently during development - but that's a much longer story.

Alright, so one eye gradually moves across the skull during development. What about during evolution? Do we have any clues as to the steps involved? Well, as many biologists know, the fossil record has now answered the question for us.

In a well-known study that was published last summer in Nature and received much media attention, Matt Friedman showed findings from a series of fossils delineating a clear gradual evolution from symmetrical to asymmetrical flaltfishes. (For excellent in-depth coverage looking at this study and the debate over flatfish evolution, see one of my favorite science bloggers, Ed Yong at Not Exactly Rocket Science, and also see the popular science writer Carl Zimmer at The Loom, and GrrlScientist at Living the Scientific Life).

Flatfish Evolution

Flatfish Evolution (Friedman 2008)

The evolution of the flatfish eye seems to mirror what we see during development. Thus, here we have a case of ontogeny appearing to recapitulate phylogeny quite wonderfully. There are many excellent examples of this throughout the biological world, though few that show such incredible similarity between the two processes of development and evolution. Nonetheless, this isn't really evolution we're watching during flatfish development - we're merely seeing how slight changes of the developmental programs are themselves responsible for the changes we see over time through evolution. Generally speaking, earlier developmental processes appear much more similar across varied species than later processes.

Development is in fact one of the primary constraints against evolution.

So while you were never a fish, you still showed remnants of fishy development during your own development. For it was these fishy developmental process that allowed the evolution of your own.

Scientific References:

Previous Adaptations of the Week:

  1. Timber Rattlesnake Camoflage
  2. The Aye-Aye’s Freaky Finger (I’ve Been Cursed by an Aye-Aye!)