Dinosaur Color: No Longer a Wing and a Prayer

by Jennifer Frazer on February 6, 2010

A previous artist's wild guess at the colors of Anchiornis huxleyi. In a (to me) earth-shattering development, scientists now have a real idea of its colors -- go to the first article linked to below for the new image.

Something happened this week and last that I never thought I’d see in my lifetime — or ever. Scientists discovered the colors of some dinosaurs.

After the first article I saw, I figured it was a one-time fluke. Then this week, I saw this article about Anchiornis huxleyi close on the heels of this article last week about the tail strip colors of Sinosauropteryx, and I knew it was the real deal. For feathered dinosaurs at least, we now have a time machine. As I commented on the New York Times, the moment of realization brought a tear to my eye. I took a course on dinosaurs in college. I vividly remember our professor stating how color was just something there was no way of knowing and would always be up to our imagination. That was just 10 years ago.

How did they do this? In modern birds, feathers have pigment sac shape and arrangements that hold constant for various colors of modern birds. Since most (but not all) scientists believe birds descend from one group of dinosaurs, they looked at feather-like bristles on the fossils of bird-like ancestors. Sure enough, the familiar melanosomes were there and interpretable. Of course, melansome arrangement, pigment, and shape may have changed slightly over 100 million years, but my gut feeling is that they wouldn’t change too much given the laws of physics presumably haven’t either. Sharks still look like they did 150 million years ago, so things don’t necessarily have to change.

Of course, the color of dinosaurs with scales continues to elude us. But who knows? 10 years after deciding to go to the moon, we walked there. We put our mind to eradicating smallpox and now that virus exists only as a few samples frozen in little plastic tubes in U.S. and Russian labs. Scientists discovered the scaly mummified remains of a duck-billed dinosaur in Montana in 2002. With enough determination and good science, there may well be a way.

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I can’t say enough about the work of Jacques Perrin. The French filmmaker has been making nature documentaries of the highest order since 1996, when “Microcosmos” was released (though unlike films I will mention later in this post he only produced, not directed the film). The film, a triumph of bringing the daily dramas of the small and insectivorous to humans everywhere in gorgeous slow-motion closeups, is still perhaps the best nature documentary I have ever seen. This is so because Jacques Perrin’s documentaries are not only works of science, they are also profound works of art.

Yes, I like this even better than the work of my beloved David Attenborough (though Planet Earth [the David Attenborough version] comes in a close second for my best nature documentary of all time). What sets “Microcosmosapart is the way that the filmmaker, in a wordless, observational way, connects us to his subjects and their apparent joys and sorrows. That and the famous opera-scored, erotic snail love scene. Run, do not walk, my friends, to see this if you have not.

Then six years later he produced “Winged Migration”, another stunning yet nearly wordless work of art that was an order of magnitude better than the popular favorite “March of the Penguins” released a few years later*. Again he displayed his talent for engaging us emotionally in the lives, struggles, and wonders of being a bird.

Though I still prefer “Microcosmos” (insects are more intriguing to me than most birds), this film has also stuck with me. I’ll never forget the moment when a sage grouse first performed (WARNING: SPOILER. Do not click link if you plan to see the film. Which I hope I have convinced you you should) its mating tupperware burp and Dolly-Parton-inspired ladies’-man dance in the film (clip not from the film but this must be seen to be believed). The whole audience gasped, and then laughed. Several years later I was lucky enough to see this live when I moved to Wyoming.

So it was with great excitement that I read today that Perrin has released a new film in France, “Oceans“, that is dominating the box office. I cannot, cannot wait until it surfaces here.

From the Time Magazine article on the film:

Most French reviewers seem to agree, however, that Océans is Perrin’s most effective work yet in terms of evoking solidarity with endangered nature. It is part of his agenda. He told Le Monde, “We’re entertainers, and I don’t want to be pretentious and start moralizing. But Océans is part of our means of persuasion. We must react urgently, protect, create blue helmets for the sea. Otherwise, humanity is headed toward an unbearable solitude.”

You all know that I couldn’t agree more. It is the philosophy of this blog too.

And in case you’re curious, if you want to see how they packaged it for “American” audiences, see here. This does not speak well of our national character, or at least what Hollywood thinks is the only way they can market to “American” audiences. Apparently, if it’s not warm-blooded and fuzzy, or involves a gripping action scene with a pounding techno soundtrack, we’re not interested. Sigh.

Still can’t wait to see the film. Yay, Jacques Perrin! The world needs as many of his films as we can get. And Jacques, in case you’re reading this, the world is ready for the first big-screen protist, slime mold, diatom, lichen, alga, and fungus documentary. Trust me. Thank you.

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* I actually felt March of the Penguins was only an average nature documentary. My feeling at the time was its popularity could only be explained by the disappearance of all other good old-fashioned nature documentaries, and people remembering what they liked about them. I’ve already talked about “The Animal Bothering Show” style pioneered fairly colorfully by Steve Irwin but copied rather lifelessly by many others. Most of these shows teach you very little coherent about nature — certainly not in the way a David Attenborough documentary does or Wild America did, calmly and quietly following the cutthroat trout through the seasons of its life for a year, inviting you to meditatively take in the sound of the bubbling brook as the fish goes about the business of life. Then again, I’m a nerd. I probably wouldn’t get bored at an 8-hour Proust lecture. : )

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The One Cell Planning Commission

by Jennifer Frazer on January 31, 2010

Efficiency in Motion: A wild slime mold clambers over soil and moss looking for bacteria and protists to eat. Note the dead leaf for scale. http://www.flickr.com/photos/deliciousblur/ / CC BY-NC 2.0 Not for commercial use.

Behold, the artful amoeba itself — a slime mold. In this case, it is Physarum polycephalum, the lab rat of plasmodial slimes. Scientists in Japan have been leading the world in creative slime mold research, demonstrating about 10 years ago (when I was first learning about these creatures) that slime molds could solve mazes. If you’ll recall, slime molds can also remember. We’re talking about an oversized bag of multinucleate cytoplasm here, folks. (Cytoplasm being, of course, everything inside a cell membrane, and multinucleate because it contains lots of nuclei, or DNA packets) So it was no surprise to me to see the latest juicy morsel of slime mold research last week, once again from Japan, showing that not only can slime molds efficiently design rail networks, they can do it for a budget comprised of a $2.99 box of oats. Planning engineers, prepare for Japanese outsourcing.

The slimes managed a decent reproduction of the actual Tokyo rail network when scientists put a piece of the mold where Tokyo would be inside a Japan-shaped corral with oat flakes placed at the location of major cities. To simulate mountains or other barriers that slime molds have no way of knowing about, they illuminated portions of the map. Slime molds, like vampires, trolls, and college students, hate light. In just over a day, the slime mold had taken in the lay of the land and laid down its solution to the problem. The similarities were striking. For a map of the actual Tokyo rail network versus a slime-mold-designed network, see here (scroll down).

Slimes do it by spreading out in all directions, moving on from areas without food and pumping more cytoplasm into the ones that do. For a great video of the slime mold doing its thing in the experiment, see here.

So you see, slime molds would never miss that left turn at Albuquerque. They’d take both turns. : ) Boringly, the scientists designed a computer program to replicate the effect that they hope could help design mobile and computer networks without human help. I don’t understand why they don’t just stick with slime molds, though. “Will work for oats — prefer nights” makes for a pretty attractive employee in my opinion.

By the way, the “oat flakes” they talk about in this study are just regular rolled oats. Though you might be tempted to think the slime molds are eating the oats, they are not. They eat the bacteria that live on the oats. Yes, your oats have bacteria on them. No, this is not cause for panic. In spite of what the makers of Chlorox would have you believe, germs are a normal part of our world. More on that another time . . .

To see how most slime molds fit in to their section of the tree of life, go here and look for “Amoebozoa”.

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Your Daily Parasite Fix: The Corpse Flower

by Jennifer Frazer on January 26, 2010

Since any parasites you may be hosting are at this moment getting their daily fix of you, why not get your daily fix of parasites? It turns out that in honor of the International Year of Biodiversity, a parasitologist at the American Museum of Natural History is hosting a Parasite of the Day blog — that’s right! One parasite a day for the entire year. By the end you’ll be totally sucked dry.

The one that blew me away was the parasite that has evidently converted itself (or rather, has been converted by evolution) from a snail into a worm-shaped set of gonads, much like adult tapeworms (or guinea worms!). The chief way scientists know it is a gastropod is its larvae — which still appear as “tiny, delicate snails.” Evolution: Totally Frickin’ Crazy/Awesome.

Still, just to prove that not all parasites are insects, worms, worm wannabes, or politicians, here is a plant parasite that I used to stumble upon all the time in the murky gloom while mucking around upstate New York forests hunting mushrooms and other oddities: Monotropa uniflora, also called Indian Pipe.

Monotropa uniflora (once-turned single flower, I think), also called Indian Pipe, Ghost Flower or (most luridly) Corpse Flower. Photo by liz west, Creative Commons Attribution 2.0 Generic License.

You see, parasitism can happen to anyone — even a nice flowering plant like Monotropa. Its flowers are the bulbs at the end of the curled-over stems, above. It is usually ghostly white or sometimes pink (though I’ve never personally seen a pink one) because it has no more need of chlorophyll, the chemical that allows most plants to convert sunlight into food. It has found a way to parasitize the fungi collectively called mycorrhizae (miko-rye’-zee) that are cooperative with nearly all trees (and, in fact, nearly all plants!).

Since the mycorrhizae get most of their food from the tree they are helping support, this little flower is in effect parasitizing the trees it grows under. Its proximal victims tend to be mychorrhizal fungi in the family Russulaceae (Roo’-syu-lay-see-ay or Russ’-you-lay-see-ay), which contains the prolific genera Lactarius and Russula. If you’ve ever been in the woods odds are you’ve seen the mushroom fruits of these fungi. Russula sp. tend to make very common but mostly inedible chalky white mushrooms with red caps and white spores that frustrate North American ’shroomers looking for better, more edible fare. In Russia, they pickle and eat some. No accounting for taste (or cast-iron stomachs), I suppose.

Monotropa itself is in the blueberry or heath family, also called Ericaceae (Eric-ay’-see-ay, which you can see placed among its relatives here). This family contains many familiar berries, including blueberries, cranberries, lingonberries, and huckleberries (alert Val Kilmer). Members of this family usually prefer the acidic soils of peat and bogs often have  “urn-shaped” flowers in which the petals are all fused (botanists would say the  corolla, or whorl of petals, is united), which you can see in these blueberry flowers.

Vaccinum (blueberry) flowers. Photo by Thomas Kriese. Creative Commons Attribution 2.0 Generic License. Click image for link.

Though the petals of Monotropa aren’t united, they are clearly urn shaped, as you can see more clearly in this photo of the pink variant.

Note the bright orange pollen on the stamens around the dark-colored stigma and style, the tube that leads to the ovaries below. Photo by Magellan nh, Creative Commons Attribution 3.0 Unported License. Click image for link.

Since I moved out west I have not seen M. uniflora, though it allegedly does occur here. On the other hand, I see two other ghostly-pink parasitic plants all the time — pinedrops, also in the heath family, and spotted coralroot, an orchid (which also parasitizes mushrooms in the Russula family).

I seem to have written my way into an unplanned series on parasites. Let’s see if I can write my way out of it next time. Hmmm. I’m sensing slime molds in our future . . .

POTD discovered via The Loom.

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Gorgeous Corkscrews from Hell

by Jennifer Frazer on January 22, 2010

So I haven’t managed to get around to writing the post I had bee. . . look! Shiny! Spirochetes!

"Treats? Where!?" The social bacterium Treponema pallidum. (Subtle, very subtle)

This one goes out to those of you who think all bacteria are either boring rods or balls. (BTW, is it just me, or does this video have a strange first-moon-landing-recording-esque quality?)

Eat your heart out, physicists, engineers and animal behaviorists — you can’t say you’re not impressed here. Wave forms? Relaxation pattern? Forward and reverse? Not bad for a tidy .5 x 5-250 micrometer package. In case it’s still not clear, spirochetes (spy’-row-keets) are helical bacteria, and one of their members is the infamous Borrelia burgdorferi, the party behind Lyme Disease, the species in the video above. So is Treponema pallidum, the maker of Syphillis (TM). That’s right. Don’t mess with the ‘chetes.

Well. . . maybe not. In spite of what you might think from our highly skewed sample size of 2, most spirochetes are not nasty human parasites. They are free-living, oxygen-avoiding, bread-winning, welfare-eschewing bacteria. Incidentally, Spirochetes represent a happy accident of taxonomy. In the old days, microbes often got classified by shape. So all the spirochetes got lumped together. Turns out that actually reflects true kinship in this case. Lucky us! At least one taxon we don’t have to split and relearn!

For a look at all the groups of Eubacteria spirochetes are related to, click here. Once there, you can click on “Spirochetes” for a look at some of the specific genera in the group.

Thank you, YouTube, for making such wonders freely available to us all . . .

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Extinction by Design: Guinea Worm

by Jennifer Frazer on January 18, 2010

Though I could find little about the biology of rinderpest for the last post, guinea worm is a case of the opposite: Way Too Much Information. Guinea worm inspires horror not so much by its life history (many infectious organisms find ways to wander about your body at will), but by its size, Homo sapiens-escape method, and terrifying treatment.

So how does one go about acquiring a guinea worm? I’m glad you asked. It all starts with a copepod. During its life, an aspiring guinea worm must pass through both humans and a freshwater copepod. Remember the bioluminsecent bomb firing marine copepods I covered here?

I need a wall-mounted set of copepod antennae to impress my guests. Hook 'em, 'pods!

I need a wall-mounted set of copepod antennae to impress my guests. Hook 'em, 'pods! Photo by Uwe Kils. Creative Commons Attribution ShareAlike 3.0 License. Click for link.

Well, this isn’t one of them. It’s another marine copepod species, but the best I could do right now by way of illustration. Marine copepods, in turn, have freshwater cousins, and these cousins are hosts for the young aquatic guinea worm larvae. After a few weeks in the copepods, the larvae are ready. Drink this water without filtering out the copepods and congratulations! You’ve just acquired your own pet guinea worm, and will become host to one of the most gruesome human parasites on Earth.

For when the copepods hit the stomach, the acid dissolves the copepods but not the guinea worm larvae. Instead, the females migrate to the lining of the small intestine, burrow through, get knocked up by tiny males who then die and dissolve, and then grow into two-foot long spaghetti strands that spend a year sightseeing your body. I don’t know about you, but the only entities I want roving my body are blood, immune cells, and the occasional miniaturized submarine.

Strangely enough, you usually don’t notice all this until the worm is full term, about a year after you drank their larvae. When the blessed moment arrives, the worm migrates to a patch of skin most commonly located on feet or legs, but which can also include “the head, torso, upper extremities, buttocks, and genitalia” (eep!) and release chemicals that cause a searingly painful blister to form, which then pops. Mrs. Worm emerges — but just her tip. The pain is so intense victims are driven mad by desire to plunge the extremity into cool water. When they do, the worm immediately secretes a cloudy liquid containing scores of her copepod-seeking young, thus beginning the cycle anew.

The treatment, known since ancient times, is hardly better. You take a matchstick, twig, or pencil, wrap the end of the worm around it, and then slowly pull her out a few centimeters a day, like (brace yourself) this:

Pull any faster and she breaks, defeating your efforts. It can take weeks or months to pull the whole thing out. In the meantime, your open sore can become infected by bacteria, and the pain is so bad you find it hard to move, work, or care for others. This is not a living organism that it is easy to feel sorry for anihilating.

Like rinderpest, guinea worm is an ancient scourge whose prevention has been long understood but which thrived on ignorance and poverty. All one has to do to prevent guinea worm is drink clean water, but clean water is a luxury for millions. The nuclear option is dosing local water bodies with copepod-icide. They (and anything else that happens to depend on copepods for food) can’t be happy about that. The alternative is behavior change — persuading people to filter their water through cloth (carefully checked for stray holes!) to strain out the fairly large copepods. That’s fine for adults, but often the victims are small children who don’t know any better when they get thirsty.

Dracunculus medinensis, as this pest is most formally known, is, believe it or not, a nematode, or round worm. Roundworms are distinguished from flatworms because they have a round (duh) body and true digestive tract: a tube that opens at the mouth and exits at the you-know-where. Nematodes crawl invisibly throughout your environment every day, in soil and fresh- and saltwater. They are among the most diverse groups on Earth, and probably heaviest by biomass, on earth.  They’re everywhere. I’ll never forget teaching introductory microscopy lab during my first year of grad school and seeing a very surprised nematode crawling around a dish with a thinly sliced apple we were observing. So believe me, you have almost certainly consumed many of these little guys in your day. As with most nematodes, it looked like this.

Obviously, pregnant guinea worm females are the ultra-super-uber-heavyweights of the nematode world, and, at least in my experience, atypcial. Many nematodes are harmless free-living soil-dwellers, like the Caenorhabditis elegans that has contributed so much to our knowledge of basic development and gene function. But there are also scores of nasty parasites of both plants and animals: root-knot nematodes, hookworms, pinworms, whipworms, heartworms, and Trichinella spiralis, the reason you should not eat undercooked pork. To see where the nematodes fit into the rest of the animals, click here.

In December Nigeria announced it was the latest country to be free of Dracunculus medinensis, leaving only four in Africa that are still beset. Jimmy Carter’s on the case, so you know it won’t be long. To see a slide show from Time that vividly illustrates the worm’s toll, click here, and to read the latest news about the eradication, see here and here.

And of final note, dracunculuiasis, the disease’s formal name, means “afflicted with little dragons.” Quite so. I am glad I will never experience that firsthand, I hope that soon no one else will either.

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Extinction by Design: Rinderpest

by Jennifer Frazer on January 13, 2010

Rinderpest is somewhere in this image, but the source did not describe where. If I had to guess, I'd say it's the rods and that they're packed into a host cell with a few floating free. If so, the rods also have a membrane around them that is difficult to see. Copyright held by Dr. Rajnish Kaushik, Creative Commons Attribution-ShareAlike 2.5 License.

Extinction has a flip side: eradication. We did it to smallpox (or rather, almost did it; a few samples survive in U.S. and Russian labs), and though the ethics of that are interesting to think about as an intellectual exercise, there is no question that it has relieved the suffering of millions. Scientists are on the verge of doing it again with two organisms: another virus and an infamous parasitic worm. The obliteration of either one would mark only the second time this has happened in human history, and the first in 30 years.

Rinderpest is a vicious livestock virus that has sickened hundreds of millions of cattle in Eurasia and Africa since ancient times. In herds that have never encountered the disease, it can fell nearly every animal, and it’s not a pretty death: weeping mouth and urogenital ulcers, constipation followed by diarrhea, and a struggle to breathe. Though the virus affects only cattle and related wild animals like wildebeest and giraffes, when millions of cattle die, their keepers starve.

The rinderpest virus, a paramyxovirus in the “genus” Morbillivirus, seems to be related to the measles, mumps, and canine distemper viruses. Rinderpest is an RNA virus, which means it uses the material we normally use to translate DNA into proteins as its hereditary material. For the bio geeks out there, it’s a negative-sense virus, which means the genome has to be translated into the positive sense by an RNA polymerase conveniently packed into the virion. The positive sense strand then acts as mRNA and can make all the virus’s hijack, lockpicking, get-out-of-cell-free proteins. When the virus is done replicating, new negative-sense RNA and a sampler of the appropriate proteins are then enveloped by a membrane spiked with fusion and attachment proteins that help the virus get into cells.

Every paramyxovirus has  but a single strand of RNA, on which a mere 6-10 genes lie. In Morbilliviruses, there are exactly three nucleotides (A(denine)s, G(uanine)s, C(ytosine)s, or U(racil)s) between each gene, which is incredibly efficient packaging for those of us familiar with the thousands and millions of non-coding nucleotide bases between genes in be-celled life. The order of the genes is conserved too because the virus practices “transcriptional polarity”, a phenomenon in which genes closest to the “beginning” of the RNA strand are transcribed more often than the ones at the end. That’s probably because the protein that translates the strand — the RNA polymerase — has a tendency to fall off before it’s finished. This provides cheap and easy transcription regulation, but also a strong incentive not to shuffle your genes. What I’ve told you so far applies to Morbilliviruses and Paramyxoviruses in general, but other than its mug shot, above, I can’t find out much more online about Rinderpest’s particular modus operandi.

Strangely, in spite of its prowess, the virus never succeeded in reaching the Americas. And in spite of a reliable vaccine and the near elimination of the virus from Africa in the 1970s, we didn’t finish the job, and tens of millions of livestock were dying again in the early 1980s. Finally, in 1993 the UN Food and Agriculture Organization had enough and decided it was time to bring it to the virus. 17 years later, the end game is at hand. You can read more about the history of the virus and eradication effort and how close we are here (subscription required) and here to only the second intentional extinction on Earth.

Next time: Reason # 1,356 to be thankful for your local water treatment plant: Guinea Worm.

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The Sexual Disability of Red Algae

by Jennifer Frazer on January 10, 2010

For those who would like to know more about your friendly blogger, I have been interviewed by the community blog at The Reef Tank, a web site for home saltwater aquarists. In the interview, I talk about some of the peculiarities of aquatic plants and algae (including an explanation of the title of this post), what some of my formative aquatic experiences were, why I started this blog, and how an aquarium is like a hot tub. There’s more than enough to read there, so in that spirit, I’ll end this short post with an interesting picture of a red alga. Yay algae!

In spite of its sexual disability, this red alga is still very happy to see you. Close-up of Laurencia sp., a seaweed from Hawaii. Photographed by Eric Guinther. Creative Commons Attribution ShareAlike 3.0 License. Click image for link.

p.s. Speaking of algae, I just painted my hall a color I’m calling “kelp green”, but which has been less charitably described by some interloping visitors as “baby poop green”. It’s kelp! Kelp, dang it!

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. . . And we’re back. Apologies for the long delay, but after I returned from my vacation, I almost immediately plunged into the logistics of painting my entire home, and I’ve been otherwise engaged each night. But I wanted to be (among the) first to wish you a Happy International Year of Biodiversity!

Save Biodiversity And to celebrate this milestone, I now present you the fabulous solution to a mystery we all pondered last year. Remember the Unidentified Feathery Object (aka the Ninja Seaweed)? Well, I just saw a video post on the Echinoblog today (which also includes video of the infamous sea pig!) that explains everything. Though it be still ninja, that’s no seaweed. It’s a space station! Wait. . . let me check my notes . . .

Ahem. For your viewing pleasure, I present . . . the hairy sea cucumber!

Hmmm. . . hairy sea cucumbers. I see nothing suggestive in that name at all. Nope.

It’s also quite apparent no one taught these sea cucumbers table manners. I mean, come on: shoving your whole tentacle into your mouth at once and slowly licking it clean? Sakes alive!

Sea cucumbers (even hairy ones) are echinoderms, which means they’re most closely related to sea stars, brittle stars, basket stars, and sea urchins. This sea cucumber is clearly a filter feeder, catching tiny animals and plants on its tentacles, though I can’t seem to find out if it uses glue, or stinging cells, or poison, or dumb luck. For the sea cucumber (aka holothurian) family . . . er, . . tree, see here. Follow “Holothuroidea” down to see the different sorts. And just for the record, I’d never heard of hairy sea cucumbers either.

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The Sublime Dance of the Weedy Sea Dragon

by Jennifer Frazer on December 26, 2009

Snowed in and still wired  . . . so I’d like to close the year with something beautiful for you to contemplate. BBC keeps releasing short clips of “Life” on YouTube, and here is another (Dang you BBC! When will you release this in full in the states? When? When?!). Hit the resize button second-to-right in the lower right-hand corner to super-awesome-ify it, and the HD button too if you have the bandwidth.

Sigh. I’ll never forget the first time I saw leafy sea dragons (a relative of these weedy sea dragons) at the Tennessee Aquarium in Chattanooga. My mom practically had to drag me out of the room.

Sea dragons are not true seahorses, belonging instead to the seahorse sister taxon (most closely related group), the pipefish. The proper name of the group is Syngnathinae, which means fused-jaw (syn-gnath), and if you look at their beaks, you can see that their jaws are indeed sealed shut. Here’s a short BBC article discussing the Life clip you just watched.

And with that, we conclude our programming for 2009. I look forward to sharing the tiny, slimy, tentacled and beautiful with you in the next decade too. Cheers, all, and stay safe this holiday season. : ) Jen

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