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

27Feb/09Off

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?

26Feb/09Off

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”.

Flukes!

Flukes!

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.

NATIONAL GEOGRAPHIC CHANNEL EMBARKS ON AN EXPEDITION

TO REVEAL THE SECRET KINGDOM OF THE BLUE WHALE

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 http://channel.nationalgeographic.com/episode/kingdom-of-the-blue-whale-3302.

20Feb/09Off

Pseudonymous No More – The Big “Reveal”

I've decided - it's time for me to come out of my pseudonymous virtual closet.

Earlier this year I attended the ScienceOnline09 conference - a conference attended by over 200 science bloggers, educators, journalists, and researchers.

One of the sessions concerned online identity and posed the question "should individual bloggers keep their online identity anonymous or pseudonymous, or should they consider it as an extension of their professional life, writing under their true identity?" Of course, each individual is different and there can be many real and valid reasons for not broadcasting one's true identity. Many people write about controversial subjects (particularly those writing on the incompatibilities or intersections of science and religion). Others simply write on topics that may conflict with their professional positions or institutional missions.

After much thought, I've decided that I do not see any of these reasons as applying to me or my writings. After the conference, Andrew, the Southern Fried Scientist, wrote an excellent piece concerning his own identity, essentially making the same arguments and coming to the same conclusion that I do here. I'll start by quoting Andrew, as I could not have said it better (it's hard to say anything better than he can say it):

"Two sessions that got me thinking about the direction of my own blog were centered around transitions in your blog as your career progresses and whether or not to maintain anonymity (and how one goes about doing that). For me, I’m using this blog as a tool to create a track record of public outreach and education, and to voice my opinions on various marine, mycological, and mundane issues. Since I’m using it as a mechanism for career building, I see no reason to be anonymous (in this case that would actually be counter-productive)."

I see this blog in very much the same light (minus the ocean and fungi). I do not write about the details of my current scientific research (that is, as a government researcher I make sure that there are no conflicts of interest between this blog and my job). I rarely talk about religion or controversial subjects these days (I have a few much older posts that delve into the subject and aren't particularly controversial, but I now try to strictly avoid it).

In fact, I think the goals of this blog and of my writings have evolved to become a critical aspect of both my professional and personal life: namely the goal of bringing the grandeur of nature and science to the masses. Most of my writings are of the general science and biology variety (such as my Adaptations of the Week), often written with the laypublic in mind.

I initially took the handle "Irradiatus" during the beginning days of widespread internet use (mid-nineties) - and I've used it ever since. I don't even recall where it came from. When I started this blog (or a version thereof under a different name many years ago), it was nothing but a mental release - just a fun, inane, ranting, and completely unread by anyone exercise in self-expression. Thus, I stuck to my handle out of habit and ease.

But no more.

Thus, I now announce that my real name is Daniel D. Brown (my name is too common to not include my middle initial).

*Cue psychologist wife: "you sound like a narcissistic crazy person." I'm not. I just thought it was a funny announcement.

I am currently a post-doctoral researcher at the National Institute of Environmental Health Sciences (studying brain development), and sometimes an Adjunct Assistant Professor of Biology at Elon University. I received my Ph.D. studying the genetics of heart development in the lab of Dr. Frank Conlon at the University of North Carolina at Chapel Hill.

I have updated my "About" page if you want more information. If you link or refer to me, I don't really care which name you use. I will still be posting under my handle (much as Andrew maintains his "Southern Fried Scientist" identity), but that's mainly because my real name is lame and common. Of course, most of my regular readers know my real name already, and most of you probably could care less who I really am anyway.

12Feb/09Off

Darwin Day Linkfest – My Favorites

Though we are nearing the end of the "official" Darwin Day celebration, considering Charles Darwin's 200th birthday and the 150th anniversary of the publication of The Origin of Species, 2009 is sure to be the Year of Darwin. In fact, a slew of events will be filling the entire month of February and there are bound to be internets full of evolutionary goodness throughout the year.

The entries for the Blog for Darwin "blog swarm" are only just beginning to roll in. In this post, you will find my favorite Darwinian entries.

First and foremost, I would like to ask you all to read my own post, Darwin and the Heart of Evolution, which recounts a simplified evolutionary history in the development of our cherished organ - the heart.

On to the link love!

  • The Beagle Project Blog gives their own rundown of the best Darwin posts, here, here, and here.
  • The Digital Cuttlefish sings us the single most amazing science song ever written. It is pure beautiful poetry. Everyone should read it and hang the lyrics upon their wall.
  • Richard Wiseman Blog brings us an amazing afterimage optical illusion of Darwin himself  - a great alternative to the ubiquitous and similar Jesus illusion.
  • Observations of a Nerd explains why she is not a "Darwinist" (and why no one should be, really). As I like to say, Evolutionary Theory is to Darwinism as the blue whale is to Pakicetus.
  • If I ever gave Valentine's Day a second thought, I would most certainly give this Valentine's Day Card to my wife (hat tip to The Oyster's Garter). Thankfully my wife views the wretched holiday in the same light as I do.
  • FYI: Science! tells a great tale of teaching evolution in high school biology classrooms.
  • The Southern Fried Scientist and WhySharksMatter over at Southern Fried Science, and Kevin Zelnio of The Other 95% and Deep Sea News have begun a massive undertaking, celebrating both Darwin's birthday and the Origin's publication in November: They are growing beards from scratch between now and November for "The Great Darwin Beard Challenge". Now that's some dedication!
  • Life Science Tools of the Trade gives an incredibly entertaining look at Darwin's methods of specimen collection. In Darwin's own words (describing a rare and now critically endangered fox), "He was so intently absorbed in watching the work of the officers, that I was able, by quietly walking up behind, to knock him on the head with my geological hammer."
  • It's Alive!! speaks of Darwin's ecological villainy. It's in the same vein as the previous link - you just have to read it - short and very funny. Excerpt: "Darwin did eat a bunch of endangered turtles, lizards, birds and other animals during his voyage. It’s one of 10 fun facts about Darwin. Hah! Take that vegans."
  • Mike of 10,000 Birds gives a beautiful rundown on why birders should love Darwin.

Those are all the posts I've managed to read through thus far. I am certain that many new and wonderful posts will arise over the coming days, my favorite of which I will continue to add to this post.  Cheers! And have a Happy Darwin Day!

10Feb/09Off

The Firefly and the Deer – “Moonbeam Death Ray”

Since, it seems that I've been on an art post kick for the last two days, I thought I'd toss one more out for you. This is on oldie for me, but I'm betting that few if any of my current readers have seen it.

Way back in 2006, a buddy of mine (Joshua Robertson) was in a band called "Bronze Fawn," a progressive, instrumental group based in Seattle.

One of their songs (9 minutes in length) was called "Moonbeam Death Ray". Listening to it in the car one day, I had a "vision" (i.e. a cool idea).

I had just recently picked up a copy of the 3D computer animation software, Maya 7. So I thought, "what better way to learn to animate than by practicing with my idea for Bronze Fawn. I'm sure they will appreciate the surprise video!"

That, in essence, is how the following music video was made.

Josh was more than a bit surprised.

The video was written, directed, and animated by me with Maya 7 Unlimited. It took 200 hours over 4 months plus 600 hours of computer render time (i.e. I would set up the render and let my computer crunch out the stills while I was at the lab finishing my PhD). I modeled and textured the deer and firefly based on deer in my yard and fireflies I caught. I initially mixed the song down to its current 3 minutes length.

The YouTube version of this video has currently been watched about 478,000 times.

I have many, MANY problems with the animation (like some horrible deer movements, texture problems, lighting, etc...), but overall I was pretty happy with it for a first animation.

If anyone wants to learn animation - I say just do it.  Download the free and opensource Blender software and start doing tutorials!

My interest in animation started when I needed a good animation for my dissertation defense on frog heart development. This was the result (intended to be illustrative, NOT 100% accurate - and yes, that is what early Xenopus larvae look like):

And one more just for fun (no sound).

"Feeding Time"

You can see more of my animations HERE.