The Artful Amoeba

rescue pile

Jennifer Frazer — Tue, 30 Nov 1999 00:00:00 +0000

Of course, that doesn't mean it didn't take some figuring and tweaking to get the moss this far. On the contrary. For instance, to overcome any problems that might result from heavy-weight proteins too big to get through the lattice-like cell wall, the scientists designed a new moss bioreaktor system that allows them to strip off the cells' walls and replace them with a stabilizing chemical called alginate. But such cells can't withstand the shear forces of stirring, and stirring could complicate industrial-scale production. The authors of the paper designed a new moss bioreaktor (see Figure 5) to overcome this. As we say in biology, you can never have too many bioreaktors. It seems to probe what happens when two people who love each other dearly cannot see eye to eye on these matters, and when they must both contemplate an eternity spent apart. These are questions that sober-minded people surely struggle with just as much today. And they also adapted a clever regulatory system using baker's yeast (Saccharomyces cerevisiae) that brings a whole new meaning to the term "spooky action at a distance". They could actually dial product protein production up or down by inserting a mammalian(?) regulatory DNA sequence that responds to the chemical acetaldehyde. This chemical is a step on the way to ethanol -- the business part of good-old-fashioned booze. As is well known, yeast make ethanol from sugar, and part of the acetaldehyde gets into the air. By varying the distance between the moss and the yeast, the scientists were able to control the amount of protein produced: the closer the moss was to the yeast, the more protein it made. Three kingdoms working together here. So very cool. [Biogeek alert] Filoviruses are negative sense RNA viruses, which means they have to make a complementary copy of their genomes in order to reproduce their proteins and RNA. Their RNA encodes seven proteins, and they also apparently cover themselves in host membrane as they exocytote themselves out of the host cell. [/Biogeek alert]

What the Heck is a Rudist Bivalve? And Why Were There So Many of Them?

Jennifer Frazer — Tue, 30 Nov 1999 00:00:00 +0000

Osedax worms

Jennifer Frazer — Tue, 30 Nov 1999 00:00:00 +0000

get their bacteria from somewhere, not known, with each new generation (not inherited) like lichen get their algae!!

Look before you leap

Jennifer Frazer — Sat, 07 Mar 2009 23:29:53 +0000

Hi. You have reached the blog of Jennifer Frazer, science writer and overenthusiastic naturalist. Thanks for checking in! However, I'm not actually officially here yet as I'm still working on getting this thing designed, so you will have to be patient. There will be plenty of great amoeba/protist/lichen/zygomycete/ctenophore/bdelloid rotifer action coming very soon. I just don't want to officially launch it until I get the look I'm . . . well . . . looking for.

In the meantime, here's a great picture of an artful amoeba, the gracefully named Chaos diffluens, which has officially dethroned my previous favorite scientific name, Borrelia burgdorferi (the spiral bacteria that cause Lyme Disease). If I were an amoeba and had a name this bad a**, I'd have it tattooed on my pseudopod.

: An amoeba named "Chaos". Great name for a Western?

chaos_diffluens

Jennifer Frazer — Sun, 08 Mar 2009 05:58:16 +0000

slime_mold_olympic_national_park_north_fork_sol_duc

Jennifer Frazer — Mon, 30 Mar 2009 02:45:13 +0000

A yellow slime mold at Olympic National Park.

Today this leaf . . . tomorrow the world!

Jennifer Frazer — Mon, 30 Mar 2009 02:51:29 +0000

Ed. note: This is a repost from facebook. I'll be reposting a few things to get this blog kicked off. Apologies to those who have already seen it! j.f. Many of you know about my slightly (ok, entirely) unnatural slime mold obsession. They're weird, cool-looking, and semi-sentient. And they're even here in Colorado! I found three or four different species when on the Mycoblitz in August up at Rocky Mountain National Park. They've even been used as robot brains. (see http://www.newscientist.co m/article/dn8718) [caption id="attachment_24" align="alignleft" width="300" caption="A yellow slime mold at Olympic National Park."][/caption] Not bad for a giant crawling multinucleate bag of protoplasm. Well, here's further proof of just how cool they are: http://discovermagazine.com/2009/jan/071 Even slime molds can remember. So how on Earth is a feat like this possible for an organism that's never even heard of a neuron? I'll leave that for us to ponder. . . because no one really knows.

479px-giardia_lamblia_sem_8698_lores

Jennifer Frazer — Mon, 30 Mar 2009 02:59:35 +0000

A micrograph of Giardia lamblia.

479px-giardia_lamblia_sem_8698_lores1

Jennifer Frazer — Mon, 30 Mar 2009 03:18:53 +0000

Giardia lamblia

Thwarting "Beaver Fever"

Jennifer Frazer — Mon, 30 Mar 2009 03:19:52 +0000

I give you . . . Giardia. [caption id="attachment_39" align="alignleft" width="383" caption="In spite of what you're thinking, this is not the love child of a squid and a kernel of corn."][/caption] Also known as *cough* beaver fever (since the dam rodents are common carriers) to those hikers unlucky enough to have a run-in with this extremely unpleasant organism. Symptoms include such pleasantries as "projectile vomiting" and "explosive diarrhea". Fortunately, I do not speak from personal experience. This baby is the primary reason that all you outdoorspeople have to bother with bulky or foul-tasting water decontamination apparati. Unfortunately, it's more than just annoying to people in countries with raw sewage washing down the street, who would probably gladly bother with bulky or foul-tasting water decontamination apparati if they could afford it. So an article in the New York Times last week described a fascinating new vaccine strategy for defeating this and many protozoan parasites that rely on "coat switching". Giardia has about 190 coat protein genes. It only needs one to function. Normally, it cycles through them one at a time about every 10 generations, yanking the rug out from your immune system each time. Someone had the bright idea to make the organism express them all at once, vastly condensing the time required for your immune system to learn them all from several lifetimes to several weeks. Neat! http://www.nytimes.com/2008/12/16/science/16giar.html Its coat protein selection system is a prime example of how evolution has produced plenty of inefficiencies and life is not "perfect" (as if we needed a reminder). Instead of selecting one of its coat protein genes and only transcribing that, it transcribes *all* of them, and destroys all but the one it wants. Kinda like making dinner by cooking every recipe in the cookbook, and then tossing all the dishes but the one you're actually having. And that's not the only weird redundancy, according to the article. Giardia has two nuclei. No one knows why.

20070817111827amoeba_psf

Jennifer Frazer — Mon, 30 Mar 2009 03:54:34 +0000

A diagram of an amoeba.

20070817111827amoeba_psf

Jennifer Frazer — Wed, 01 Apr 2009 05:38:34 +0000

A diagram of the parts of an amoeba.

20070817111827amoeba_psf1

Jennifer Frazer — Wed, 01 Apr 2009 05:40:23 +0000

A diagram of the parts of an amoeba.

About

Jennifer Frazer — Wed, 01 Apr 2009 05:41:16 +0000

[caption id="attachment_126" align="alignleft" width="380" caption="A successful morel hunter and her haul"][/caption]

The Short, Short Version

This is a blog about biodiversity and natural history, although I dislike that first term. I think it turns people off to the subject. It's too often used for boring platitudes about species richness that tell you nothing about what's actually out there. I'm here to work on fixing that. I anticipate updates to this blog 1-2 times a week. If I know it will be longer, I will let you know!

The Slightly Less Short Version

Several years ago I worked as a weeder and waterer in a small family-owned garden center. One day a man came in asking for an ostrich fern. I led him back to the shade plants where we kept our selection of about five ferns. As I sorted through the chaos, he remarked, "I had no idea there were so many kinds of ferns!" According to my copy of "Plant Systematics: A Phylogenetic Approach", there are about 10,000 fern species. And we are lucky if the public recognizes there are five. The discovery of DNA was inarguably important for biology. The revolution it inspired in taxonomy was equally so. But we have lost something in the years since. The Victorians had their flaws, but one thing they did well was natural history. That's something we don't do so well. There's an unspoken bias in biology against studying "taxonomy". It's all just semantics, some might say. I say: it's not the fine print of the taxonomy that's important to 99% of humans. It's what taxonomy represents -- learning about the diversity of life on Earth. We don't have to go to Mars to find living wonders, and though I respect those that want to, I wish the 100% real living organisms on Earth could get half the attention the putative creatures on a planet millions of miles away do. The curiosity cabinet is long gone, but the curiosities are still here, just waiting for us. All 10,000 ferns. All 70,000 known fungi. All untold millions of species on Earth. I want to show you. I'm passionate about this stuff, and I like to make it fun. Please join me.

So Who Are You, Anyway?

My name is Jennifer Frazer, and I'm a science writer living in Boulder, Colorado, land of Subarus, microbrews, and overpriced outdoor gear. But Lord, how I love it. I have a bachelor's degree in biology with a concentration in systematics and biotic diversity from Cornell University, a master's degree in plant pathology with a concentration in mycology (also from Cornell), and a master's degree in science writing from MIT. I set out to be a scientist, but like many science writers, realized in horror that I didn't want to spend the rest of my life in a windowless lab staring at racks of Eppendorf tubes filled with clear liquids. That's not why I became a biologist. So I took a different path, one that led me through grad school in science writing, three months as a reporter intern at The Courier-Journal in Louisville, Kentucky, three years in Wyoming as the health and environment reporter at the Wyoming Tribune-Eagle, and finally here to Boulder, where I work as a science writer for a large science nonprofit. In 2007, I won the AAAS Science Journalism Award in the small newspaper category for work I did into the investigation of a swarm of mysterious elk deaths in Wyoming (thank you, Robert Lee Hotz!) You can see my four-minute acceptance speech here and you can get the links to the story on my Portfolio page. In my spare time, I do all manner of outdoor activities from caving to skiing to mushroom hunting to snowshoeing to climbing ridiculously high peaks where boiling water would not cook a wet noodle. And I do this. This, truly, is what gets me out of bed in the morning: sharing my excitement about all the amazing creatures that share the planet with us. And I promise -- you will be amazed. Jennifer Frazer Ardent naturalist, science writer, and finder of very exciting slime molds

My science lineage on NPR!

Jennifer Frazer — Wed, 15 Apr 2009 03:11:39 +0000

So most of my friends (and probably most of you here) have figured out I'm a bit, well, extra excited about fungi. Well, the person who planted the spore in my brain (and the person who trained her) hit the airwaves and Interwebz today after Cornell (Alma mater A) published a press release about the return of some rare Chinese fungi to their home. Here and here are print versions of the story, and here is a version that aired on NPR today (thank you Kathie and Daniel for the links!).

Kathie Hodge, the Cornell herbarium's director, said the fungi are invariably tiny -- "just dried up leaves, most of them, or pieces of wood with a little dot on them. To an average person, they look like something you would sweep off your kitchen floor. But under the microscope they're beautiful and exciting and incredibly diverse." "I think it's really important to understand the diversity of life on Earth and we are so far from being able to do that right now," she said. "And fungi are one of the last great frontiers of biology."

These rare fungi just made it out of Dodge before the Japanese played havoc with the country during the Sino-Japanese war prior to World War II, and the stories imply had it not been for the heroic efforts of a Chinese Cornell alum to sneak them out of the country and ship them to Ithaca, they would all have been lost. Instead, they headed to Cornell where they met a fate similar to the Ark of the Covenant at the end of Raiders of the Lost Ark: warehousing in the Cornell Plant Path Herbarium (I don't mean to imply that's a bad thing -- quite the contrary! Although I did once visit the Herbarium, and I have to say, it was very mothbally). The story of what happened to their valiant rescuer is sad, though, and a testament to the brutality of the Cultural Revolution. I've seen several movies that portrayed it, at least in part, including The Red Violin and Farewell My Concubine. I never cease to be appalled. Here's hoping the current Chinese government can put these specimens to good use (though if you read carefully, you see we are keeping half of each sample just to be on the safe side). Lord knows the ecology of China is not what it once was. It occurs to me that these specimens provide the hope that if some have gone extinct, we might at least be able to perform the Jurassic Park treatment.

morelhunting

Jennifer Frazer — Wed, 15 Apr 2009 03:17:29 +0000

morelhunting1

Jennifer Frazer — Wed, 15 Apr 2009 03:17:59 +0000

The Fish with the Observation Deck

Jennifer Frazer — Wed, 22 Apr 2009 05:00:24 +0000

Back in March, I posted a link on Facebook to this blog, the aptly named, "Scientists Solve the Mystery of Why this Fish is So Freakin' Crazy", at the Deep Sea News. The blog includes this clip: If there was ever a fish that belonged on Futurama . . . this is it. The see-through head apparently protects the fish's eyes from the stinging sea creatures it steals its food from. I knew there was a reason I keep a pair of safety goggles in my kitchen; you never know when the soup will shoot a nematocyst-covered stinging tentacle your way . . . see Better Off Dead. But then on Monday, DSN posted a new link to -- amazingly -- a Colbert Report clip about the fish. Just so you know, Colbert's reaction is pretty much how I feel about all the crazy organisms I'll be writing about on this blog. To wit:

The Colbert Report

Mon - Thurs 11:30pm / 10:30c

Craziest F#?king Thing I’ve Ever Heard - Barreleye Fish

colbertnation.com

Colbert Report Full Episodes

Political Humor

NASA Name Contest

If this clip won't load, you can find the DSN version here. Oh, and just for the record, the fish's latin name, Macropinna microstoma, roughly translates to "Big wing little mouth".

amoeba_big

Jennifer Frazer — Fri, 24 Apr 2009 00:14:29 +0000

amoeba_big1

Jennifer Frazer — Fri, 24 Apr 2009 00:15:07 +0000

myriorama_hemitrichia

Jennifer Frazer — Fri, 24 Apr 2009 00:44:16 +0000

slimemoldfinder

Jennifer Frazer — Fri, 24 Apr 2009 00:45:46 +0000

aug-oct2008-005

Jennifer Frazer — Fri, 24 Apr 2009 00:48:30 +0000

aug-oct2008-0051

Jennifer Frazer — Fri, 24 Apr 2009 00:49:16 +0000

jenphotocrop

Jennifer Frazer — Fri, 24 Apr 2009 00:51:15 +0000

The Header Image

Jennifer Frazer — Mon, 27 Apr 2009 03:26:25 +0000

This is the wasp nest slime mold, Metatrichia vesparium, as captured by photographer Kim Fleming in Abbeville County, South Carolina. The image was retrieved from flickr and used on this site with her permission. Slime molds are social amoebae that exist as solitary cells before mating/fusing into a collective called a plasmodium. After wandering the earth like Cain terrorizing innocent bacteria, they rise up into fantastically beautiful fruiting bodies where they produce spores that seed the wind with little amoebae-to-be. The Artful Amoeba is a reference both to their clever, astounding behavior and beautiful forms. Oh, and one other thing. In spite of their name, slime molds are NOT molds. They're aliens. Just kidding.

wiki_bdelloid_rotifers

Jennifer Frazer — Tue, 28 Apr 2009 03:00:23 +0000

wiki_bdelloid_rotifers1

Jennifer Frazer — Tue, 28 Apr 2009 03:13:06 +0000

wiki_bdelloid_rotifers2

Jennifer Frazer — Tue, 28 Apr 2009 03:14:47 +0000

Lesbian Necrophiliac Bdelloid Rotifers (and the Scientists who Love Them): Part 1

Jennifer Frazer — Thu, 30 Apr 2009 03:47:12 +0000

So you've been having a rough decade eking out a living as a bdelloid rotifer, living in the soil, some moss, or a small vernal pool. First, it stopped raining a few days after you hatched. Then you entered a period of dried-up stasis in which your cell membranes ruptured, metabolism ground to a halt, and DNA may have been cuisinarted. Bummer. But lucky for you, it started raining! And guess what, it's raining genes! (Cue The Weather Girls) Which is great news, because your species is all female and hasn't had sex in 100 million years. Hallelujah! [caption id="attachment_150" align="alignnone" width="547" caption="Scanning electron micrographs showing morphological variation of bdelloid rotifers and their jaws. We're going to need a bigger microscope (apologies to Roy Scheider and Peter Benchley). Photo by Diego Fontaneto, available under a Creative Commons Attribution license. Click photo for link."][/caption] As described in this little article over at discovermagazine.com, without a way to exchange and recombine genetic information, many animal species tend to degenerate and disappear over time (thus the joy of sex) because they lack efficient ways to generate novelty that can help them adapt to changing environments. That's OK -- when you're a bdelloid rotifer, you can do it Hoover style: just vacuum up whatever stray DNA happens to be in your environment, including the genes of whatever it was you might have recently had for dinner (note to self: glad am not bdelloid rotifer). Plants, animals, bacteria, fungi, and who knows? -- you might even get lucky. You might manage to incorporate some variant versions of your own species's genes, thus escaping the cruel grind of creeping genetic obsolescence. Coming soon: Part 2: So what is a bdelloid rotifer anyway?

rotifer_habrotrocha_rosa

Jennifer Frazer — Tue, 05 May 2009 04:04:17 +0000

rotifer_habrotrocha_rosa_alien

Jennifer Frazer — Tue, 05 May 2009 04:59:25 +0000

rotifer_habrotrocha_rosa_alien1

Jennifer Frazer — Tue, 05 May 2009 05:03:00 +0000

OLYMPUS DIGITAL CAMERA

Lesbian Necrophiliac Bdelloid Rotifers (and the Scientists who Love Them): Part 2

Jennifer Frazer — Tue, 05 May 2009 05:30:47 +0000

So what is a bdelloid rotifer anyway? As you can see from the photomicrographs in the previous post, they are not going to be trying out for the Flyers anytime soon. Rotifers are among the simplest, smallest animals. In less than half a millimeter they pack in about a thousand cells, including a primitive nervous system (we're talking like 15 cells here. "Rotifer-brained": for times when "bird-brained" just doesn't cut it), digestive system, and foot with -- incredibly -- toes. Let's put it this way: rotifers are multicellular animals that are smaller than some ciliated protists (protists include this blog's titular amoebae and other high school biology favorites like Paramecium). They're called bdelloid because they inch along like a leech -- yes, bdelloid apparently means leech-like, as in, "Attack of the Giant Bdelloids." Just doesn't quite have the same ring to it as this. They're called rotifers (Latin: wheel-bearers) because they have a crown of little beating hairs called cilia surrounding their head that they use to suck in food -- suspended organic particles, protists, or other small animals. Even more impressively, some rotifers have a toothed organ inside their mouth called the mastax that they use to grind food, and which they can actually sometimes evert to snare dinner. [caption id="attachment_198" align="alignnone" width="500" caption="An artist's interpretation of mastax eversion by a bdelloid rotifer. Any resemblance to Ridley Scott films (living or dead) is purely coincidental. Original image by rkitko, available under a Creative Commons Atribution license. Click image for link."][/caption] Rotifers have resurrectional powers rarely matched on Earth. After the typically fatal DNA- and membrane-shredding treatment incurred by drying up, they can somehow, once wetted, mend hundreds of DNA breaks and simply swim off. Even more jaw-droppingly, they can apparently use those same powers to withstand searing doses of radiation:

A comparison: in the most resistant arthropod[ed. note: arthropods include animals with jointed exoskeletons like insects and crustaceans] known, a 200 Gy dose produces more than 99% sterility; in bdelloids, a 560 Gy dose causing approximately 500 double-strand breaks per genome reduces fecundity by only 20%. The researchers point out that resistance to ionizing radiation may be an accidental by-product of resistance to desiccation. Both factors cause double-strand DNA breakage.

Forget balls of steel. This is DNA of steel. Why are we thinking of sending humans to Mars? Clearly, we should be sending bdelloid rotifers, who can thrive in the radiation-soaked environment of space, attack the Martians, and do it all backwards, in a high heel, and without breaking a chromosome. In any case, you may be wondering where the lesbian necrophilia comes in. I'll let the scientist at Harvard who studies these things -- Matthew Meselson -- speak for himself.

It’s likely, he says, that during recovery from dessication, bdelloids pick up genes from members of their own species, too—dead members, that is, whose genes spill out of ruptured cell membranes. That process would provide the kind of genetic reshuffling that other animals achieve through sexual reproduction. “It may be their form of sex,” Meselson says. “But their partner is essentially dead. So you’d have to call it necrophilia. Actually, since they’re all females, lesbian necrophilia.”

Kudos to you, sir, for being a scientist and not speaking like a grant application. If more scientists spoke this way, we might have less of a problem with people not giving a d--- about science. Much additional bio geek goodness can be found over at Small Things Considered. (Additional source: Purves, Orians and Heller. Life: The Science of Biology. 4th ed.)

New post tomorrow

Jennifer Frazer — Sat, 09 May 2009 13:32:14 +0000

Hi everyone. Sorry it's been a while between posts but almost all of my free time this week was taken up by preparing for a talk on lichens to some local schoolgirls on Thursday and a presentation I'm giving today at the Denver Skepticamp called "Life on Earth: The Short, Short Version." Hang in there! I'll be back soon. jf

ninja_of_seaweed

Jennifer Frazer — Sun, 10 May 2009 19:47:40 +0000

Unidentified feathery object (UFO)

Jennifer Frazer — Sun, 10 May 2009 19:52:43 +0000

Again via Deep Sea News, here's a video of a "ninja seaweed" from the Red Sea. Prepare to be impressed: This is what 600 million years of relentless predation will do for ya, folks. Nothing to see here. These aren't the . . . whatevers . . . we're looking for. Move along. Guesses on the identity of this bad boy over at DSN ranged from some sort of cnidarian (like a soft coral or anemone) to a sea cucumber or even some sort of fancy sea turtle extra-option package. Your guess is as good as mine. Anyone here want to take a (groan) poke?

moss_bioreactor

Jennifer Frazer — Fri, 15 May 2009 02:14:21 +0000

physcomitrella_patens_moss

Jennifer Frazer — Fri, 15 May 2009 03:27:54 +0000

physcomitrella_protonema_moss

Jennifer Frazer — Fri, 15 May 2009 03:32:27 +0000

wiki_meketre_cattle_model

Jennifer Frazer — Sat, 16 May 2009 20:49:08 +0000

wiki_plowing_farmer_egypt_sennedjem_cattle

Jennifer Frazer — Sat, 16 May 2009 20:56:33 +0000

wiki_meidum_geese_oldkingdom_egypt

Jennifer Frazer — Sat, 16 May 2009 21:09:17 +0000

Ancient Egypt lives on -- thanks to Trixie and Ralph

Jennifer Frazer — Sat, 16 May 2009 21:50:25 +0000

Though cattle wouldn't ordinarily grace the pages of The Artful Amoeba (vertebrates in general being a bit boring for my taste), I make an exception today. In the Denver Post was an article about the birth of a new ankole calf named Belle at the Denver Zoo to proud parents Trixie and Ralph (yes, of Honeymooners fame). Take a look. Awwwwwwww . . . . . but as a female mammal, I must say Thank God the little darlings are born SANS horns. *Shudder*. The breed is also called Egyptian longhorn, but before I even got to this detail in the article, I was struck by how closely these cattle resemble the cattle Egyptians actually depicted in and on their tombs: [caption id="attachment_285" align="alignnone" width="611" caption="Photo by Gérard Ducher, distributed under a Creative Commons attribution license. Click image for link."][/caption] The cow second from left looks a lot like Belle. This model is from an incredible collection found in the the Middle Egyptian tomb of a noble called Meketre who died ca. 2000 B.C. In his tomb in a secret room that tomb robbers missed were found intricate dollhouse-like models of soldiers marching, sailors rowing, brewers brewing, bakers baking, or Meketre himself counting his cattle. Meketre had all these models placed in his tomb so all these things could happen for him in the next world. Together, they form an intimate, detailed snapshot of daily life in ancient Egypt. If you're ever at the Met in New York City, don't miss their share of the collection. Here's the nobleman Sennedjem with Egyptian cattle as seen on his tomb wall: [caption id="attachment_289" align="alignnone" width="575" caption="The artisan Sennedjem plows heavenly fields on his tomb wall. Ca. reign of Seti I/Ramesses II, 1200s B.C."][/caption] I've always loved those splotchy cattle with the big horns I see in Egyptian art. It's nice to know that even though the builders of the pyramids and their culture are long gone, their cattle, at least, live on. And while we're on the subject of animals in Egyptian art, I've also been struck by the contrast between the formal, stiff poses Egyptian artists used to depict humans, and the Audubon-esque naturalism with which they sometimes precociously depicted animals. They had a keen eye for detail, as you can see in this painting of geese made almost 5,000 years ago during the Old Kingdom. [caption id="attachment_291" align="alignnone" width="600" caption="Geese painted in the tomb of Nefermaat and his wife Atet during the reign of the triple-pyramid building Pharaoh (and Ladies' Man) Snefru, ca. 2600 B.C."][/caption] Just for the record, this panel of geese (not all are shown here) may be my favorite work of Egyptian art ever. Its simplicity, attention to detail, balance -- and may I say grace? -- are timeless. As far as I know, no other culture came close to this level of artistic excellence and realism for several thousand years (though hard to know, since most ancient art has gone way of dodo). This was a first for the world. And, one might also argue, for scientific illustration. Hope you enjoyed a little art history and Egyptology with your biology. We'll be back to our regularly scheduled programming tomorrow. Jen

wiki_pink_dragon_millipede

Jennifer Frazer — Wed, 20 May 2009 03:40:47 +0000

What You See When You Drink Too Much in Thailand

Jennifer Frazer — Wed, 20 May 2009 04:10:25 +0000

[caption id="attachment_306" align="alignnone" width="500" caption="I love the smell of cyanide in the morning. Smells like . . . Desmoxytes."][/caption] Because nothing says, "Don't Eat Me!" quite like a neon pink millipede (unless you're two, in which case it says, "All You Can Eat Candy Buffet!"), I give you: The Pink Cyanide Millipede. In addition to its easily pronounceable Thai (Mangkorn chomphoo) and Latin (Desmoxytes purpurosea) names, it features a pleasing almond aroma (courtesy of the cyanide it's oozing). Pink millipede saté sticks, anyone? To see more bizarre animals either discovered or more fully investigated in the last few years (including our old friend the barreleye fish and the can't-miss flesh-eating ghost slug), check out this gallery of bizarre animals over at New Scientist. You'll be glad you did!

email-address

Jennifer Frazer — Wed, 20 May 2009 04:30:09 +0000

Portfolio

Jennifer Frazer — Wed, 20 May 2009 04:33:02 +0000

Hire Me

I am a science writer who speaks, writes, and blogs on natural history and the diversity of life. If you're interested in hiring me as a speaker, freelancer, or guest blogger, write me at

Speaking

You can see my first public lecture, "Life on Earth: The Short, Short Version", here.

Interviews

I gave an interview to the Reef Tank in January 2010 on the peculiarities of aquatic plants and algae, what some of my formative aquatic experiences were, why I started this blog, and how an aquarium is like a hot tub. Read it here.

Writing

"Technology: Audio Recording Systems" on the National Association of Science Writers' All About Freelancing website, September 22, 2009: bit.ly/VQD5y (NASW members only)

Work from my time as health and environment reporter at the Wyoming Tribune-Eagle in Cheyenne (in reverse chronological order):

My AAAS-award winning story on mysterious mass elk deaths in Wyoming, November 26 and December 3, 2006: Part One Part Two There was a sidebar on the science of the guilty party, but it was never posted online.
More red than green, September 9, 2007. The Mountain Pine Beetle's Excellent Adventure.
Rocket Test, June 28, 2007. Who knew Wyoming had an aerospace industry? In an abandoned missile silo. Really!
Wyoming gets its state grass, April 1, 2007. Not an April Fool's story, but I did write this one with tongue planted firmly in cheek.
A step closer to ancient England, March 27, 2007. In this story, I talked to an émigré from England who decided to build a medieval mead hall in the middle of the prairie. By himself. Irony: The zoning laws in England would have prevented him from doing the same thing there.
Fawns emigrate south, June 15, 2006. I found myself running full tilt across the prairie in business casual next to a guy with a giant-butterfly net attempting to capture pronghorn fawns for this story. A personal favorite.
Medicine Bow clear cutting debated, May 1, 2006. I climbed into a single-engine aircraft and flew over the Medicine Bow National Forest to report this story.
8,900 pounds of elk -- free and Lines greet free meat, April 13, 2006. The Wyoming Department of Game and Fish decided to give away 33 35-50 pound boxes of culled elk meat to the first 33 people to show up on a certain day. Some stories write themselves.
Stormy program begins in Wyoming, August 22, 2005. All about the science of cloud seeding. Wyoming is perhaps the first entity on Earth to have both the need and means to conduct the first scientifically valid test of cloud seeding, which has never been scientifically proven to work, according to a National Academy report that came out just a few years ago.
Great divide, April 10, 2005. Won 1st place for Environmental Story in the National Newspaper Association 2006 Better Newspaper Contest, Daily Division. A story about the conflict over oil and gas drilling in the Red Desert. I got to go on a tour of this extremely remote but gorgeous desert for the story -- and it stands out in my mind as having the most startling explosion of lichen diversity I've ever seen. Plus we passed a sheepherder's wagon complete with Belgian draft horses, anthills that reached to my knees, and herds of wild horses. Let no one tell you being a reporter in the west doesn't have its perks.
What's next for the sage grouse? May 15, 2005. The plight of the sage grouse in oil and gas country. Complete with exciting sage grouse lekking action.
Girls' guide to the galaxy, May 11, 2005. A conference designed to spark girls' interest in science.
Meet the Unmakers, January 24, 2005. A look at e-cycling in Cheyenne at a place called . . . wait for it . . . Tatooine Electronic Systems.

And finally, my very first story ever --

Scientists Work to Preserve Apple Diversity, Cornell Daily Sun, November 15, 2001.

Brief resume: Education A.B. with Distinction in All Subjects, Cornell University 2000. Major: Biology, with a concentration in Systematics and Biotic Diversity. Phi Beta Kappa. M.S. Plant Pathology, Cornell University 2002. Concentration in Mycology. M.S. Science Writing, M.I.T., 2004. Work Experience Science Writer, The National Center for Atmospheric Research. 2007-present. Health and Environment Reporter, The Wyoming Tribune-Eagle. 2004-2007 Reporter Intern, The Courier-Journal, Louisville, Kentucky. Summer 2004 Intern, Focus, Harvard Medical School. Spring 2003 Staff Writer, The Cornell Daily Sun. 2001-2002

Moss That Swings Both (All?) Ways

Jennifer Frazer — Sat, 23 May 2009 15:00:34 +0000

I'm sometimes greatly amused by the quality of press release science writing that is taking the place of professional science writing these days, since no one will pay for us to do it full time anymore (Science Daily, a major source of internet science news, is made almost entirely of press releases reprinted verbatim. And you'll notice that this very blog is, so far, gratis). For instance, a press release on one of the coolest things I've seen in a long time includes this sentence, seemingly lifted from Timmy's 3rd grade report on mosses:

At first glance, mosses and human beings have little in common.

Gee, ya think? I'm imagining myself at a coffee shop holding a cup of steaming tea and sitting across the table from a noticeably uncomfortable bryophyte. [caption id="attachment_249" align="alignleft" width="608" caption="Cough. *Blink*"][/caption] Me: So, read anything interesting lately? Moss: No. See? Not much in common. Strangely, this doesn't differ greatly from most of my actual dates. I don't want to seem too hard on the author here, since 1. the release was probably first written in German, and 2. this is actually one of the clearer and more helpful press releases I've read. In any case . . . Scientists from ETH Zurich and the University of Freiburg im Breisgau report that they were able to insert DNA from humans and bacteria into the moss Physcomitrella patens (sounds suspiciously close to "patent") and the moss was able to manufacture human proteins without any further help. Yes, they basically cut and paste. And the moss said: OK! Cool! [caption id="attachment_250" align="alignleft" width="616" caption="The protonema of Physcomitrella patens. When the spore of this moss lands on a suitable spot, it starts growing into filaments like these. Given enough time, these little filaments will grow into a full-grown moss plant. You can see the chloroplasts, or light harvesting equipment, as little green circles."][/caption] For those of you unfamiliar with the Way of the Cell, DNA makes RNA (with the help of proteins called RNA polymerases), and RNA makes proteins (with the help of cell organelles called ribosomes). The reason this moss-cular feat is astounding is that doing the same thing with flowering plants will get you nada. The mammalian gene start and end sequences have evolved themselves right out of business when placed in a similarly much-modified flowering plant. Not that there's much of a reason that that would *ever* happen in nature. Now in an evil mad plant scientist laboratory, on the other hand . . . Belgians + petunias = Brussels sprouts. Mwa ha ha ha ha ha . . . . . How is it mosses can do what so-called "higher" plants cannot? It's a mistake to think of mosses as "primitive" in the sense of "inferior". Both mosses and flowering plants have ancestors that were alive at the same time. What mosses are is "less-derived", in biologist-speak. The lineage that gave us mosses just didn't change as much over time as the lineage that produced flowering plants, because they found they were well-adapted as-is to their particular niche (forests, rocks, sidewalk cracks, and the sets of "Lord of the Rings" adaptations). Like sharks, they found a sweet gig and they stuck with it. According to Ralf Reski, botanist and co-author of the paper announcing this discovery, as part of this cozying into a niche relatively early on for multicellular life (moss seem to have sprouted out of the ocean and then pretty much called it a day) mosses have stayed genetic generalists. And this easy-going gene-set enables them to translate a wide range of DNA. In fact, hold on to your hats . . .

This cross-kingdom conservation of mammalian and moss protein production machineries is phylogenetically profound, and has several implications for basic and applied research. Comparative genomics, as well as functional studies, have recently established major differences in metabolic pathways and gene function between flowering plants and P. patens, and have suggested that a substantial moss gene pool is more closely related to mammals than to flowering plants (Frank et al., 2007; Rensing et al., 2008). --Plant Biotechnology Journal , Volume 7, Issue 1, 2009. Pages: 73–86

Dude! An article in the Plant Biotechnology Journal just blew my mind! Who knew? Well, maybe John Wyndham. In my next post, we'll take a look at what on Earth possessed these scientists to stuff human genes into a soft, green, cushiony object and at why biology is WAY cooler than nuclear physics. Stay tuned.

The Six Million Dollar Moss: Why Biology is WAY Cooler Than Nuclear Physics

Jennifer Frazer — Wed, 27 May 2009 13:42:47 +0000

As mentioned in the last post, for some reason (actually quite a good reason we'll get to soon) scientists at ETH Zurich and the University of Freiburg im Breisgau thought it'd be a great idea to splice some human genes into . . . er, moss . . . and see what happened. Ordinarily, you'd have to finesse the DNA to get it to work in a plant. But this worked just great the first time. What's even better are the AWESOME MOSS BIOREAKTORS they used to do it! [caption id="attachment_239" align="alignleft" width="568" caption="Is that Luke Skywalker in there? The only thing that could possibly make this image more awesome would be some lightning shooting out of the tops of those reaktors (cannot help self -- the Germanic K is too much fun). Eat your hearts out, nuclear physicists! Click image for source."][/caption] Now I ask you, does it get any cooler than bionic moss? Although this does beg the question: Why, on God's Green Earth? Because this bizarre, dissociated, barely recognizable moss could provide a cheaper, easier and more economical way to produce drugs like insulin. Right now such proteins are produced in relatively costly and difficult-to-maintain mammalian cell cultures with organic vegan-class nutritional and environmental requirements. Only industrial countries can handle the complexities, and demand is outstripping supply. Moss, on the other hand, makes its own food. All it needs is some light, a few inexpensive salts, water, and room to grow. Have Chlorophyll -- Will Transcribe. A simple growth solution also makes purification of the product protein much easier, according to the paper. With such a set-up, even developing nations may one day be able to make insulin for their own diabetics. Yes, better living through biokemistry. : )

wiki_giant_isopod

Jennifer Frazer — Fri, 29 May 2009 02:07:26 +0000

paganwandererlu_isopodcover

Jennifer Frazer — Fri, 29 May 2009 02:16:40 +0000

Coming to a Benthic Store Near You . . .

Jennifer Frazer — Fri, 29 May 2009 02:38:45 +0000

I couldn't help but laugh when I saw this one, folks. But I give you the Dave Barry Oath: I Am Not Making This Up. Yes, behold: "Songs About Giant Isopods". Who needs a rousing sea chanty when you can have a rousing isopod modern rock ballad? You'll recognize such hits as, "Isopod Love Song", "Chitinous Tease", "An Isopod is Cute in the Eyes of an Isopod", (including the immortal lyric, "Just because we're not as cute as kittens and things, doesn't mean we deserve to go extinct.") and "Giant Isopods Ate My Well Known Brand of Corn Chips." Does it make you think less of me if I admit I like, "Isopod (I can evolve)"? So what's a giant isopod? Well, they're crustaceans (like shrimp, crabs, and lobsters) in the same taxon with woodlice, aka pill bugs. Yes, they are essentially foot-long, seafaring pill bugs on steroids. The wander through the deep ocean scavenging carcasses or attacking slow-moving prey. Oh, and if you're ever in North Taiwan, you can apparently have one of them for dinner. I need a giant isopod bib. [caption id="attachment_400" align="aligncenter" width="330" caption="Don't hate me because I'm beautiful."][/caption] Discovered thanks to Deep Sea News.

Films about Giant Isopods

Jennifer Frazer — Sun, 31 May 2009 16:41:05 +0000

Because you can never have too much David Attenborough . . . here is a short clip from Planet Earth that shows our giant isopod friends from my last post in action. It's kinda like an all-you-can-eat buffet down at the Sizzler. Mmmmmm. . . carcassy. . . . Love that crab at the end.

Attn Science Bloggers: 3 Quarks Daily Science Blog Post Contest

Jennifer Frazer — Sun, 31 May 2009 18:10:50 +0000

I've entered my first moss post into a science blog post contest over at 3 Quarks Daily judged by Stephen Pinker. If you're a science blogger, it's not too late to enter one of your posts either, although you have to hurry. The nominations close at midnight on June 1. Check it out!

ants-003

Jennifer Frazer — Tue, 02 Jun 2009 03:10:47 +0000

Ants Going Nuts

Jennifer Frazer — Tue, 02 Jun 2009 14:37:27 +0000

As I was on my way back from work on Friday, I noticed a strange black mass on the pavement near my house. It was like a soccer riot -- ants crawling all over apparently trying to beat the snot out of each other. I half expected to see some broken beer bottles and tiny torn Manchester United T-shirts lying around. Occasionally one would fall off the edge of the curb in a Wilhelm scream-worthy fall. Check out the video, in which if you look carefully, you'll see three take a spill: I've seen pile-ons like this once or twice before in my life, and I assume it's a fight between rival colonies. But I'm not an entomologist. Does anyone here know what these ants are up to?

wiki_trilobites_heinrich_harder

Jennifer Frazer — Wed, 03 Jun 2009 03:51:21 +0000

Voting Opened at 3 Quarks Daily

Jennifer Frazer — Thu, 04 Jun 2009 03:13:00 +0000

Voting is open in the 3 Quarks Daily Science Blog Post Contest I entered last week. There are over 100 entries (including little ol' mine!), so if you're interested, take a look and vote for your favorite! You have until midnight on June 8.

wiki_trilobite_heinrich_harder

Jennifer Frazer — Thu, 04 Jun 2009 13:31:38 +0000

A Stirring and Beautiful Journey Through Time

Jennifer Frazer — Thu, 04 Jun 2009 13:48:34 +0000

It's been 4.5 billion years since Earth formed, and oh, what a long, strange trip it's been. National Geographic photographer Frans Lanting has created a beautiful slide show set to music about the evolution of life on Earth to help you experience it in considerably less time. The online version consists of 86 photographs with crisp captions that follow the history-of-life artistic tradition of the Rite of Spring from Fantasia (check out the amoeba!) and any number of other museum murals and books. It's a pleasing sensory experience, something akin to a brain back rub, if such a thing is possible. I have only a few quibbles; the Cretaceous seems to have been a particularly groovy era of Earth history based on its inexplicable 70's-game-show musical interlude, and there are a few inaccuracies (i.e. the spacing of the pictures in the time line is SO not to scale; chlorophyll does not fuel all life). But these are minor and beside the point. He has also created a live action version featuring music by Philip Glass and "images, dance[ed. note -- I'm suddenly envisioning giant isopod be-costumed dancers prancing across the stage], film, and science." The premiere will be June 10 in New York City, and will include as guest of honor one of my three science heroes -- E. O. Wilson (love you E.O.! Wish I could be there to meet you!) -- along with a slew of other stars and scientists including Alan Alda, Harrison Ford, and James Watson, the Watson half of Watson and Crick (the guys who along with Rosalind Franklin figured out the structure of DNA). The online slide show does suffer a bit from the common problems of the genre laid out by Stephen Jay Gould in the preface to his Book of Life; first, the omission of "simple" creatures like microbes, invertebrates, and fungi from the show after vertebrates appear, with the attending implication that they stop evolving after their appearance. On the contrary. Invertebrates, fungi (actually, fungi never even appear in the show except as lichens), microbes and ferns have all continued evolving and adapting. One diorama at the Denver Museum of Nature and Science featuring conifers from the late Paleozoic/early Mesozoic shows conifers with shockingly (to my eyes) broad leaves. Needles only evolved later. The second problem is the implication that evolution is a predictable and inevitable march of increasing superiority resulting in the evolution of Homo sapiens, the be-all end-all. It's hard to get around this problem, though, since it's nice to highlight major novelties (and let's face it, flowering plants, mammalian diversification, and humans were indeed major novelties) in chronological order, and humans did arrive very late on the scene. Finally, there is the problem of time distortion, magnified in this case by the skewed presentation of the time line. For most of Earth's history (probably the first 3 billion years anyway), life was simple and microbial. But we get only a handful of pictures devoted to that, and dozens of pictures devoted to the last 500 million years. It'd be a pretty boring slideshow if he didn't present it this way (if for no other reason than we don't have much information about what that early life looked like), but it's a distortion nonetheless. Would it be so hard to make the timeline to scale, anyway? Check out the slideshow first, but when you are done looking at it, check out the timeline. Choosing each image reveals extras including Lanting's notes on the pictures and often some cool bonuses like video of the geyser or stromatolites. In spite of my (and Gould's) quibbles, it's a first rate production! As always, I, and I'm sure he, hope you will draw inspiration from the beauty of life to help protect it. Discovered thanks to Carl Zimmer at The Loom.

wiki_sperm_whale_sucker_scars

Jennifer Frazer — Sat, 06 Jun 2009 13:57:42 +0000

wiki_pakicetus_arthurweasley

Jennifer Frazer — Sat, 06 Jun 2009 14:35:44 +0000

Dude, Where's My Cod?

Jennifer Frazer — Sat, 06 Jun 2009 15:10:44 +0000

Anyone who's spent time fishing can tell you that every so often, after patiently waiting hours for a bite, one will reel in one's line to discover that somehow, someone has pilfered the bait. Apparently Alaska black cod fishermen have a problem along the same lines(so to speak), although in this case it was the catch that was purloined, and not the lure. So someone rigged up a camera to capture the thief in flagrante. Take a look at this video that came across the National Geographic newswire a few weeks ago: Wait for it . . .

No, that is not a sawblade attached to an oven mitt. That, mateys, is a sperm whale. And not just any sperm whale. A sperm whale that has learned to rob lures of bait without hurting itself or using fingers, fins or tail. Pretty slick! Sperm whales are the largest toothed predators on Earth. They dive deep in search of squid and fish, and judging from the sucker scars sometimes found on their skin . . .

. . . they really do get in battles with colossal squid deep underwater. Their heads contain a massive organ filled with a waxy substance called spermaceti. In the 19th century, this, along with oil from the whale's blubber, was prized for making candles as affordable as tallow but far less smoky, lamp oil, soap, cosmetics, crayons, and a number of other products. The spermaceti's actual purpose may be buoyancy control (the whale hardening it to dive and liquefying it to rise), echolocation, or both. Since these whales aren't afraid of defending themselves by using their head as a battering ram, a few actually did manage to sink some whaling ships in the Pacific, including the Essex in 1820, which inspired Melville to write Moby Dick, and the Ann Alexander in 1851, which was attacked (after, it should be said, first attacking the whales) about the same time that Moby Dick was published, and probably helped to market the book. What is really extraordinary, when you think about it, is that these behemoths evolved from a small furry, doglike creature that existed 55 million years ago. [caption id="attachment_533" align="alignnone" width="616" caption="An artist's reconstruction of Pakicetus, an ancestor of modern whales. This image by Arthur Weasley is distributed under a Creative Commons-attribution license. Click image for link."][/caption] What an amazing world we live in! In any case, so long as you're not shooting harpoons at them or swimming around looking tasty at 6,000 feet, sperm whales are probably mostly harmless. Here is a film of a sperm whale calf (who doesn't seem to have teethed yet) to give you a closer look.

Weird + Cute³ + Old Spice = ?

Jennifer Frazer — Wed, 10 Jun 2009 13:53:07 +0000

Saw this over at Zooillogix and couldn't resist. I cannot believe Jim Henson did not design this creature. I also cannot get over the impression that somehow, this thing looks like a cranky old man with his pants hitched up too high.

According to wikipedia, jerboae are "jumping desert rodents" from North Africa and Asia. Tasty and bite-sized desert rodents, too, I'd wager. Perfect for kebabs . . . The jerboa, together with kangaroo rats of North America and hopping mice of Australia, are a great example of convergent evolution. This often happens when organisms from very different lineages evolve to fill similar niches, like whales and fish, or fungi and oomycetes (water molds -- an oomycete, for example, caused the Irish Potato Famine). Two mammal posts in one week! Never thought that would happen. I must be going soft.

My First Biodiversity Talk

Jennifer Frazer — Sun, 14 Jun 2009 17:27:06 +0000

The title of this post was inspired by John Cleese (with a dash of Scrubs). When I was in school in Ithaca, Cornell named him an honorary professor and invited him to speak at our interfaith chapel. I showed up on Sunday to find the title of his talk in plastic stick-on letters on the sign outside: "John Cleese -- 'My First Sermon'". Back in May, I saw a call by a group of skeptics I belong to for talks at their annual meeting, the Colorado Skepticamp. The talks could be on any sort of skepticism OR on any discipline of science. One of my aims is to speak publicly and frequently on the sorts of things I blog about here, so I jumped at the chance. My idea was to do a quick survey of life on Earth hitting all the major groups in less than 30 minutes, so I called it (with apologies to Mel Brooks), “Life on Earth: The Short, Short Version." So here you go -- My 23 Minutes of Fame. There are two versions. One has better sound: And this version has higher resolution: I made a few mistakes for which I hope you'll forgive me. . . all I can say is this was my first time giving this presentation and it's hard when your mouth is moving faster than your brain. I have noted them below. If, after watching it, any of you are interested in having me/hiring me as a speaker, I'd be happy to make it longer or shorter or elaborate on any taxon that interests you. : )

Errata/Clarifications

I mentioned that Hennig changed the way we do taxonomy by suggesting evolution as our grounds for classification. What I forgot to mention is the way that evolutionary history has now become largely judged by DNA and not always so much by what the organisms look like, where they live, etc. The byzantine circular taxonomic trees I presented were created using DNA sequences – and molecular taxonomy now dominates classification (it's not always the last word, but it's almost always the opening sentence). But for all of our scientific efforts, judging the true evolutionary history -- especially when different pieces of evidence conflict -- can still be a bit of an art.
The slide where I show some differences between bacteria and archaea shows a few of the differences between these groups, but there are many more. Don't think by any means that these are the only two. I mentioned this earlier but not at this point.
Flu viruses are in Orthomyxoviridae, not Paramyxoviridae. It's the taxon directly above the one I point at. I was in the right neighborhood but again, the mouth was moving too fast for the brain. This is what happens when you try to cram life on Earth into 23 minutes.
Operculum is Latin for a little lid or a cover, not Greek for cap. I knew what I meant, I just didn't say it right.
Moss spores are haploid, not diploid. Meiosis occurs in the the sporangium in the top of the sporophyte.
I seem to imply all cup fungi shoot their spores in a cloud but that's not accurate. Many cup fungi don't. Even the ones that do may not if they're not in the mood. In this respect, they aren't so different from. . . er . . . never mind.
I got a little confused on jellyfish but remembered soon after the talk what the problem is: jellyfish do not have alternation of generations in the same sense plants do. Both forms are diploid (the sperm and egg fuse before dividing further), but they do alternate between sexual and asexual organisms.
And finally, I looked it up and Venus's Girdles are indeed bioluminescent at night. Sorry.

Muchas gracias to Mile High Skeptics for making generously recording and sharing my lecture!

Wiki_Phallus_impudicus

Jennifer Frazer — Thu, 18 Jun 2009 12:21:07 +0000

wiki_800px-Phallus_hadriani_eggs

Jennifer Frazer — Thu, 18 Jun 2009 12:51:09 +0000

Say, Is That a Stinkhorn in Your Pocket . . . ?

Jennifer Frazer — Thu, 18 Jun 2009 13:00:12 +0000

[caption id="attachment_604" align="alignnone" width="574" caption="The stinkhorn Phallus impudicus, a species native to Europe and North America, looking happy to see us. Photo credit: Jean-Pol GRANDMONT/Creative Commons Attribution Sharealike 3.0 license. Click for link."][/caption] All right, gentlemen. Show of hands. How many of you would be proud to have a two-inch, foul-smelling, penis-shaped fungus named after you? Really? Well, Robert Drewes, curator of herpetology at the California Academy of Sciences, was certainly pleased as punch. He was the leader of a biodiversity survey to the African islands of Sâo Tomé and Príncipe. When one of his mycologist buddies discovered a new species of stinkhorn, whose genus name, Phallus, pretty much says it all, he decided to name it after Drewes, who already has a snake and frog named after him. Click here to see a picture of Drewes's Phallus. It's quite beautiful, actually. Boy, never thought I'd say that in public. Stinkhorns are basidiomycetes, one of the four major groups of fungi. This group includes mushrooms and boletes (mushrooms with pores underneath instead of gills) and a whole bunch of other interesting fungi we won't go into right now. Stinkhorns start out as little eggs, sometimes called "witch's eggs", that are considered edible delicacies by many cultures. They don't stink when they're little, I've been told. [caption id="attachment_607" align="alignnone" width="571" caption="Would you eat this? Me neither. Cross section of a stinkhorn egg of Phallus hadriani, photographed in California. Photo: Nathan Wilson. Published under a Creative Commons Attribution ShareAlike 3.0 license. Click image for link."][/caption] But within a few days, the eggs pop open and the "shameless phallus", as Linneaus called it in Latin, arises from the forest floor. The head is covered in a sticky, carrion or dung-smelling, olive-colored spore mass called the gleba, in which passing flies delight in wallowing. They then spread the spores via the friendly skies.

wiki_Lamellibrachia_luymesi1

Jennifer Frazer — Tue, 23 Jun 2009 13:46:39 +0000

To Boldly Go Where No One Has Gone Before (On Planet Earth)

Jennifer Frazer — Tue, 23 Jun 2009 14:33:04 +0000

Today I give a Pseudopod Salute to ocean explorer Bob Ballard, discoverer of the Titanic, who gave one of the best plain English explanations of tube worms and the importance of ocean research to Stephen Colbert back in February I have ever heard, and seems like a genuinely nice guy to boot:

The Colbert Report

Mon - Thurs 11:30pm / 10:30c

Robert Ballard

www.colbertnation.com

Colbert Report Full Episodes

Political Humor

Stephen Colbert in Iraq

And what is the most important underwater discovery Ballard's helped make? Not the Titanic. "The new life forms we found." Amen, brother! The life forms in question include the famous Riftia pachyptila, or giant tube worm. Riftia does indeed have "human-like blood" containing hemoglobins similar to ours but also able to bind oxygen in the presence of sulfur (which can be the tube worm bacterial partner's food), something that would kill most of the rest of the hemoglobin-using world. Giant tube worms are also among the longest-lived animals on Earth, capable of living over 200 years. They're in the same phylum as earthworms -- Annelida -- who also have hemoglobin containing blood. Riftia has tube worm relatives that live shallower in the sea, too. But don't get the impression these are the only deep-sea worms we've found. There are many species adapted to feed on differing parts of the veritable all-you-can-filter buffet of chemicals that ooze, squirt, or jet from the ocean floor. Take, for instance, Lamellibrachia luymesi, a tube worm that lives in the Gulf of Mexico around cold oil and methane seeps. [caption id="attachment_630" align="aligncenter" width="613" caption="Lamellibrachia luymesi. Photo/Charles Fisher, Creative Commons Attribution 2.5 License. Click for link."][/caption] Since it lives at colder temperatures (and is less likely than Riftia to get wiped out by a sudden devastating change in the hydrothermal vent plumbing or an underwater eruption), it lives even longer -- and may even hold the world animal longevity title at over 250 years of age. Now I know a lot of my friends are space nuts who love NASA. Who doesn't love NASA? But I must echo Ballard: NASA's one year budget to go to places where life doesn't even exist (most likely) would pay for 1600 years of NOAA research. It just ain't fair! Think about it: we'd been to the moon for 10 years before we even knew "black smokers" and Riftia communties that live totally independently of the sun existed. What is wrong with that picture? Couldn't we do a little better for NOAA? Any lawmakers who might be reading this blog, take note: studying Earth is just as (if not more) important as studying other planets. We live here! And what's more, weird, wonderful life waits for us in countless crannies, and many of said crannies are under the sea. Let's go there (and let's line item one of these for Jen, so she can go there too. : ). Discovered via Deep Sea News.

flickr_hemitrichia_serpula

Jennifer Frazer — Fri, 26 Jun 2009 03:47:59 +0000

Lacy Double Take

Jennifer Frazer — Fri, 26 Jun 2009 04:20:55 +0000

The other day I was walking by the coffee table at work and noticed a Science magazine cover that made me do a 180. First, take a look at this. Now examine this: [caption id="attachment_660" align="alignnone" width="576" caption="Credit: George Shepherd. Used with permission; click image for link."][/caption] Striking, no? And strange as it may seem, neither one of these creatures was the inspiration for the Boston street "grid". Those Bostonians thought that one up all on their own. This would be, I believe, another form of our old friend convergent evolution. So what the heck are these two things? Well, the cover of Science is a closeup of a tropical coral called Favia speciosa. I believe the lacy network (scientists would call it "reticulated" or "reticulate", which is just a fancy Latin term for "net-like". Gladiators with tridents and nets were called "retiarii") is the bony calcite skeleton of the coral, the walls between each individual animal or "polyp". During the night (or whenever they get peckish), they poke their little heads out and filter feed the water with teeny, finger-like tentacles. The second image is, of course, one of my favorite -- and distinctly terrestrial -- creatures: a pretzel slime mold, Hemitrichia serpula. This is one of those plasmodial slime molds I get so excited about that starts out as two individual and microscopic amoebae in the soil who meet, have coffee, realize they share the same values, desire for spores, and that all-important "chemistry", and decide to fuse and grow into a giant, gelatinous, pulsating bag of cytoplasm that goes on an insane bacteria-eating rampage. When the time has come for the blessed event, instead of making individual bulbous sporangia (places where spores are made) like the slime mold in the photo at the top of this page, H. serpula simply freezes into a netlike structure and subdivides its entire body into a giant spore mass. I believe this structure goes by the beautiful name "aethalium" (pronounced "ee-THAL-ium". Should name first-born daughter "Aethalia"). UPDATE 7/23/09: George Shepherd informs me that this reproductive structure is a plasmodiocarp, not an aethalium. I'm working on figuring out the difference between the two, but when I do I'll post it here. After drying out, the structure splits open and a fuzzy mass of spores flies out and blows away in the wind. In the photo above, you can see this is already starting to happen.

Wiki_Harvestman_Opiliones

Jennifer Frazer — Mon, 29 Jun 2009 02:09:15 +0000

Nice Legs

Jennifer Frazer — Mon, 29 Jun 2009 02:26:00 +0000

[caption id="attachment_686" align="alignnone" width="609" caption=". . . and she knows how to use them. The harvestman (daddy long legs) Phalangium opilio. Credit: Dschwen/Creative Commons Attribution Sharealike 2.5 License. Click for link."][/caption] Sometimes evolution moves quickly and groups of organisms change radically over very short spans of geologic time. Think of modern horses, which evolved from dog-sized creatures over the course of the last few tens of millions of years. Or take humans -- we only evolved about 150,000 years ago, and if you look at our ancestors ca. 3 million years BP, you'd find yourself looking at an unfamiliar face indeed. But sometimes, when a particular organism hits on a successful niche, it changes hardly at all. I've previously mentioned that sharks and mosses fall into this category. But this week I found an interesting story about some amazing harvestman fossils that show they are in the same boat. Harvestmen, also called daddy long legs, are arachnids like spiders or scorpions. Scientists recently found two new species in fossils from north central China that date from 165 million years ago. That's right -- the Jurassic, When Dinosaurs Ruled The Earth.

The two new species, described by Selden and his colleagues in an upcoming Naturwissenschaften, were entombed in fine-grained volcanic ash that fell in what is now north central China about 165 million years ago. The harvestmen — and the ash — either dropped into a lake or were washed there soon after the ash fell, Selden notes. Little is left of those ancient harvestmen: The fossils are, for the most part, 3-D outlines of fragile bodies that disappeared long ago. Those tiny molds, however, preserved even small details of the creatures, including their mouthparts, genitals and the joints of their legs.

You just gotta love German science journal names. Wait . . . genitals? Yes. According to scientist Paul Selden, one of the authors of the paper, the details are so fine and the organism so similar to existing harvestmen, we can tell that if you saw one of the fossilized species wander through your back yard today, you wouldn't even look at it twice. And this is a creature that once may have scuttled underneath T. rex or Stegasaurus! I can't publish the photo here for copyright reasons, but head on over to Science News to see the fossil and read the rest of the article and make sure to embiggen that fossil photo -- twice. With enough time, it is amazing what low-probability events can happen.

Feed is Full Text Again

Jennifer Frazer — Tue, 30 Jun 2009 14:58:24 +0000

After experimenting with making the feed a capsule summary, I've decided (at the suggestion of Stephanie Chasteen, aka sciencegeekgirl) to go back to a full-text RSS feed. So if you unsubscribed because you were annoyed by that, it's OK to resubscribe! If you're already a subscriber, refresh the feed to see the full text of everything that's been previously published.

Darwin in Love

Jennifer Frazer — Fri, 03 Jul 2009 18:32:43 +0000

He had two loves: biology, and his wife Emma. They didn't always agree. Yes, sometime this year, we will get to see two talented actors, Paul Bettany (Master and Commander, A Beautiful Mind) and Jennifer Connelly (who was the young girl in Labyrinth, and also in A Beautiful Mind, for which she won a Best Supporting Actress Oscar), portray Darwin and his wife in the new film Creation. As this year marks the 200th anniversary of Charles Darwin's birth (who, I believe, also shared a birthday with Abraham Lincoln), the producers have impeccable timing. Also impeccable casting. Bettany and Connelly happen to be married in real life. And I have great faith in Bettany's ability with this type of material: if you have never seen his turn as Darwin-class naturalist and British naval physician Dr. Stephen Maturin (who happens to get to (briefly) visit the Galapagos where he's stunned by the diversity) in Master and Commander: The Far Side of the World, Run, Do Not Walk. Ohhhhhh, Dr. Maturin. I'd sort your collection any time. I am heartened by the above trailer. Finally we will have a movie that maturely deals with some pretty sticky and intersecting subjects: science, faith, and love. These are subjects that many sober-minded people find themselves painfully grappling with even today. If it's half as good as it looks, I can't wait. Release is scheduled for some time this year, though the date has not been named. Together with The Young Victoria (if they'll ever give it a #$*@! U.S. release date!), I think we are in for a whole lot of Victorian goodness this year.

wiki_tubifex_worms

Jennifer Frazer — Tue, 07 Jul 2009 02:41:32 +0000

The Creature(s) from the North Carolina Sewer

Jennifer Frazer — Tue, 07 Jul 2009 02:59:20 +0000

Every so often, an organism comes along that has even biologists fighting over what it "is". Now you'd expect that after several thousand years of scientific inquiry, we'd have a pretty good handle on the terrestrial macrobiota of the world. You'd be wrong. The background here is that a North Carolina construction company was hired by the city of Raleigh to inspect its sewer lines. They used a flexible periscope to snake their way in and capture video. I'm sure they never expected what they were about to find. This one is not for the faint of heart, kids. Brace yourself and hit play. Speculation on the identity of these masses has ranged from bryozoans to annelid worms and slime molds to space aliens. One thing I can say for sure is this is NOT a slime mold. No slime mold is capable of moving that quickly. To see slime molds move, you'd have to time lapse the heck out of a video. This is also not what I'd call slime mold habitat. They like water, but not THAT much water. They tend to prefer a nice soil/dead wood wrap, easy on the sunlight. Several experts queried by both Deep Sea News (where I found this gem) and ABC News (lots of good reporting here) seem to be agreeing that this is, in fact, a colony of Tubifex tubifex, or sludge worms. Here's DSN:

Enter stage right Dr. Timothy S. Wood who is an expert on freshwater bryozoa and an officer with the International Bryozoology Association. I sent along the video and this was his reponse…
Thanks for the video – I had not see it before. No, these are not bryozoans! They are clumps of annelid worms, almost certainly tubificids (Naididae, probably genus Tubifex). Normally these occur in soil and sediment, especially at the bottom and edges of polluted streams. In the photo they have apparently entered a pipeline somehow, and in the absence of soil they are coiling around each other. The contractions you see are the result of a single worm contracting and then stimulating all the others to do the same almost simultaneously, so it looks like a single big muscle contracting. Interesting video.

So, for the record, here are what individual Tubifex worms can look like: [caption id="attachment_755" align="alignnone" width="576" caption="Matthias Tilly/Creative Commons Attribution 3.0 Unported License."][/caption] Sludge worms are annelid worms, just like tube worms, which means they have . . . wait for it . . . *human-like blood*! Combined with their filamentous form, and synchronous contractions, it really does add up to give these clusters the appearance of a pulsating heart. Or something. If you watch the video carefully (don't have anything to eat first), you can see the individual worms snaking around in that mass. According to the all-knowing, all-seeing Wikipedia, T. tubifex lives in lakes and rivers ingesting bacteria and other organic debris. Identifying them is difficult, though, because, inconveniently enough, they dissolve the reproductive organs we use to identify them when they're finished mating. "[Barry White music in background] Oh honey . . . come on over here and give me some OH WHY DO I EVEN TRY!?" In addition, their physical appearance changes based on water quality, which might explain their, well, extraterrestrial appearance in the above video. And perhaps not unexpectedly, fish apparently find these guys delicious. Sludge worms: they're what for dinner. Now with 95% more meaty slime! Hey, don't knock 'em. They'll put scales on your chest. For one last wormy treat, here is a video of the little guys fully submersed in the lab: So, I ask you: space aliens or sludge worms? You decide.

noaa_sea_cucumber_holothurian

Jennifer Frazer — Sat, 11 Jul 2009 03:31:28 +0000

What is a Sea Pig?

Jennifer Frazer — Sat, 11 Jul 2009 03:40:36 +0000

I'm so glad you asked! What IS a sea pig? Here's a hint: a sea pig is an echinoderm. No? Still not picturing it? A sea pig is in a group of echinoderms called sea cucumbers. Like this: [caption id="attachment_778" align="alignnone" width="590" caption="We have cuke sign! Get your cucumber hooks ready! NOT a sea pig, but a close relative in the same group, the sea cucumbers, aka holothurians. Photo credit: National Oceanic and Atmospheric Administration/Department of Commerce"][/caption] OK, so the short answer is that a sea pig looks like a cross between a star-nosed mole, a naked mole rat, and a hallucinogen-induced, Cthulu-themed nightmare. Except cute. Awwwwwww! Can you get a sea piggy bank? Well, not exactly, but you can get something very close: a sea-through pig. Wanna sea what I mean? To stop me from making any more bad puns, and to find out JUST WHAT THE HECK A SEA PIG IS, go here and find out all the wonderful details, courtesy the Echinoblog (via Deep Sea News). You'll be glad you did. Thank you.

UGA_salamander_07-06-09

Jennifer Frazer — Sun, 12 Jul 2009 23:27:53 +0000

How Many Salamanders Can Dance on the Head of a Dime?

Jennifer Frazer — Mon, 13 Jul 2009 04:03:47 +0000

A: At least one, if it's a U. brucei. [caption id="attachment_783" align="alignnone" width="576" caption="Not glass. Not rubber. Not made in China. 100% All-American Salamander. Now in convenient "fun size". Courtesy University of Georgia."][/caption] Remember when I said we still don't have a full idea of the terrestrial macrobiota (aka big living stuff) of the world? Here's more proof. This little guy was discovered only in 2007. Right next to a road. In broad daylight. In Georgia. This was not deepest, darkest, remotest Africa we're talking about here. The species, the adorably named patch-nosed salamander (with the slightly less adorable scientific name Urspelerpes brucei), was so different from anything else known that scientists gave it its own new genus (whose name seems to be a cross between Urkel and Purple Nurple). That makes it the first new tetrapod genus in America in 50 years. And there could be more. There are probably hundreds, if not thousands, of unnamed and unknown *visible* fungi, plants, insects, etc., right here in North America. In your state. In your county. Now when you think of the problem in the ocean or rainforest you can see how many species are biting it before we even get a chance to know they're there. But not our little friend here. Thankfully, if he ever goes the way of the leisure suit, we can at least tell our children what he looked like.

Levenson.Newton+Counter US cover

Jennifer Frazer — Thu, 16 Jul 2009 02:46:23 +0000

Levenson.Newton+Counter US cover

Jennifer Frazer — Thu, 16 Jul 2009 02:47:24 +0000

houghton_newton_hres

Jennifer Frazer — Thu, 16 Jul 2009 02:57:07 +0000

Artful Amoeba News

Jennifer Frazer — Thu, 16 Jul 2009 03:19:40 +0000

The esteemed Tom Levenson, author of the newly released (and well-reviewed) book Newton and the Counterfeiter -- and director of the Graduate Program in Science Writing at my alma mater, MIT -- has kindly featured my blogs on his with some warm words for yours truly. Thanks for the shout-out, Tom! I'll be adding his blog to my blogroll as well, along with a few other new blogs I've discovered. I'm trying to keep my blogroll useful for readers of this site by making nearly all of them related to particular groups of organisms. Today I'm adding Skeptic Wonder, a blog about protists (protists being skpetical as well as artful, obviously : ) ), The Echinoblog, which is a great resource for they of the hydrostatic skeletons, virology blog (with domain name inexplicably ending in .ws, the extension for . . . Samoa?), The Other 95%, which seems to be loosely about invertebrates and particularly marine invertebrates, and a plant blog from University of British Columbia Botanical Garden, Etaerio Botany Photo of the Day. There is a Grand Canyon-sized blogging gap in the subject of botany and plant taxonomy(please readers, correct me if I'm wrong) -- bloggers who are looking for a niche take heed!

plos_marine_bacteriophage

Jennifer Frazer — Fri, 17 Jul 2009 01:56:19 +0000

Virus as Muse, Cruft as Medium

Jennifer Frazer — Fri, 17 Jul 2009 03:04:02 +0000

This is a bacteriophage. Kind of eerie and ghostly, isn't it? It's a virus that infects bacteria, looks like the lunar lander, and was among the first viruses ever discovered. These guys may also be the most ubiquitous biological entities on the planet; you may be swallowing untold millions in every accidental mouthful of fresh or seawater. Did I mention the water's teeming with the bacteria and archaea they prey on too? Most viruses are either simple rods, spheres, or polyhedrons (often icosahedrons -- 20-sided polyhedra, of course). This baby is both and then some. In the world of virus architecture, this is the fully loaded Corvette with T-tops, all-leather seats, and pre-installed hot chick. It is a natural work of art. So why didn't someone think of this sooner? I have no idea who this guy is but I like how he thinks. There's a certain delicious irony in using old computers to build models of . . . viruses. My capsid's off to you, sir. Who needs a lawn gnome when you can have a lawn phage?

wiki_Volcano_Socompa

Jennifer Frazer — Tue, 21 Jul 2009 01:50:30 +0000

flickr_liverwort

Jennifer Frazer — Tue, 21 Jul 2009 02:46:02 +0000

The Very High Life: Part One

Jennifer Frazer — Tue, 21 Jul 2009 03:57:17 +0000

Even in a wind-blasted, God-forsaken place like the top of Long's Peak, Colorado -- 14,259 feet -- moss and lichen grow abundantly among the rocks. I've seen them there, snugly hunkered down on the acres-wide summit. This is a place that sees about a month or so of semi-balmy weather per year, followed with 10-11 months of relentless UV, ice, snow, freezing fog, blizzards, climbers, more ice, and the occasional crazed skier. Truly, there are few places on Earth life can't make it. What makes the following story (which I discovered here) so amazing, though, is the abundance of life -- veritable oases, really -- at almost 19,850 feet near the blasted summit of Socompa Volcano in the Andes. Scientists from the University of Colorado at Boulder led by Dr. Steven Schmidt recently traveled there to investigate reports of complex plant communities growing at these extremely high altitudes on volcanic vents. The nearest, albeit sparse, plants growing without the benefit of vents peter out at about 15,100 feet -- nearly a mile below. If the scientists confirmed their existence, such plant communities would be the highest known on Earth. Socompa Volcano straddles Argentina and Chile in the Atacama Desert. 7,200 years ago, it was the site of a volcanic cone collapse ten times bigger than that of Mt. St. Helens, which you can see in this image of Socompa taken from space. [caption id="attachment_849" align="alignnone" width="590" caption="Just be glad you weren't there when this baby collapsed. Courtesy NASA."][/caption] First, a little perspective on the freezing, arid death-zone that is the top of Socompa, from the paper by the CU scientists in Applied and Environmental Microbiology (subscription required):

Here, along the western slope of the Andes mountains,the hyperarid Atacama Desert extends up to 3,500 m in elevation,above which climate records for the volcanic peaks to the east,including Socompa, are scarce. In this region, summer precipitationgenerally occurs as transient snow or hail, winters are coldand dry, and vegetation is sparse and limited to between 3,500and 4,600 m elevation (4, 22). Mean annual temperatures below–5°C and precipitation of <200 mm are likely forSocompa (4, 25), and the absence of glacial features or permanentsnowfields on the mountain is indicative of the arid climate(23). The region is cloud-free throughout much of the year,which, along with the high elevation, contributes to extremesolar total and UV irradiances (39, 44). Socompa's slopes arebarren for many square kilometers, as the highest vascular plantsin the area are restricted to below 4,600 m elevation.

Let's review: mean average annual temperatures below -5°C (that's the mean?!), less than 20 cm (8 inches) of rain or snow for the year, and ~12/7 tanning-bed-turned-up-to-11 conditions. Have they checked for spice deposits? Yet the fumaroles of the volcano provide warm, moist refugia from the otherwise-forbidding land. Fumaroles are cracks in the earth where gasses let off by magma or by water heated underground reach the surface. The fumaroles on Socompa seep warmth, carbon dioxide, water, and methane. They are particularly inviting to life, the authors of the new study report, as they are not spewing steam, toxic sulfuric gases, acids, or [Dr. Evil voice] liquid hot magma [/Dr. Evil voice]. Not that a few forms of life wouldn't find a way to work around or with most of those things, but you do tend to catch more flies with honey than with boiling acid. So as I said, scientists, who for completely unfathomable reasons had failed to thoroughly investigate this volcanic Club Med previously (they seemed to find places like the Galapagos and the South Pole more inviting) finally ventured up there for a detailed look. What did they find? Wonderful things . . . which I will chronicle for you next time. Coming in Part Two: Living delights from 2/3 cruising altitude.

uwisc_jamesoniella_autumnalis_leafy_liverwort

Jennifer Frazer — Thu, 23 Jul 2009 13:32:33 +0000

uwisc_jamesoniella_autumnalis_sporophyte

Jennifer Frazer — Thu, 23 Jul 2009 13:36:57 +0000

The Very High Life: Part Two

Jennifer Frazer — Thu, 23 Jul 2009 14:47:57 +0000

Now that I've convinced you you probably shouldn't take your next vacation in the Atacama Desert (unless you're into that sort of thing, if you know what I mean), let's look at the organisms that scientists did find living and loving life in the 3 3/4 Mile-High Club. Living on the moist, warm ground were moss and liverwort gardens 30 feet across. Wait. . . liverwort? Liverworts are amazing moss relatives that can produce leathery lichen-like bodies with an emporium of odd-looking reproductive structures. They're called liverworts because supposedly, their odd protuberances can resemble livers. In medieval times, people thought that if a plant looked like something, that was God's way of telling you that it was good for treating it, a philosophy called the "Doctrine of the Signatures". So if your liver was ailing you, you might get a tincture or powder of liverwort to take. As it turns out, that's not such a great way to identify potential drug candidates, but I digress. . . The geeky-cool liverwort, likely Marchantia of Botany 101 fame. http://www.flickr.com/photos/benetd/ / CC BY 2.0 The most well known liverwort -- Marchantia -- makes fake-palm-tree-like female reproductive stalks and nail-like male ones (not pictured). It's such a successful little guy that this species has even become weedy. When I worked at a garden center one summer after graduating college (yes, the first job I got with my shiny new bachelor's degree was weeding and watering plants) it was not uncommon to find liverworts crowding the soil at the base of a plastic pot. Apparently the twice daily (at least) watering routine at plant nurseries agrees with them. In the wild, these little plants are often found growing near brooks, even here in Colorado, where I have seen them (uncommonly) growing next to streams in Rocky Mountain National Park. In the above picture, you can see another of their crazy reproductive structures, asexual gemma cups. They look like little bird nests. In the cups, little lens-shaped or spherical tissue packets called gemmae are formed asexually. When raindrops land in them the gemmae are splashed out and land on soil elsewhere. If they start growing and take root . . . voila! New liverwort. [caption id="attachment_893" align="alignleft" width="400" caption="The leafy liverwort Jamesoniella autumnalis. Used with permission courtesy of Robert W. Freckmann Herbarium, University of Wisconsin, Stevens Point."][/caption] However, that's a thalloid liverwort. The leathery projections in the photo above are referred to as a thallus or thalli (pl.), because they are undifferentiated (into leaves, stems, etc.) plant tissue. But there is a second type of liverwort: leafy. That's probably a bit deceptive because mosses and liverworts (a group referred to as bryophytes) don't have true leaves, shoots, or stems, a botanical nicety whose explanation I will spare you for now. The liverworts found atop Socompa appear to be of this type. When scientists sequenced part of their DNA, they found they were most closely related to a species called Jamesoniella autumnalis, which can be found in North America. Here is a picture of one found growing in Wisconsin. And here are its crazy reproductive structures: [caption id="attachment_895" align="alignright" width="400" caption="Can you get PBS with those? The sporophytes (spore making plant) of Jamesoniella autumnalis. Used with permission courtesy of Robert W. Freckmann Herbarium, University of Wisconsin, Stevens Point."][/caption] To keep this post from turning book-length, I'll merely mention that, believe it or not, the pointy-looking things you are looking at in this photo are a completely different organism of the same species as the plant they are growing out of. Plants do an amazing thing called "alternation of generations" in which they alternate between haploid (one copy of genes) and diploid (two copies of genes) organisms. All plants do this -- even petunias and apple trees. Where is the second plant of those species? Ahh . . . I'm glad you asked. But that shall have to remain a mystery for another day. : ) In this case, the green thing underneath has single chromosome copies, and the pointy things above have the dual, and their sole purpose, as they parasitically grow out of their parent plant, is to grow tall enough to broadcast the spores they are making inside those little black heads. The mosses that were found on Socompa were related to the copper moss (love that name!) Mielichhoferia elongata which, as far as I an tell, look pretty much like your standard moss but tend to grow on copper-rich rocks. That's not surprising, given that a few miles west of Socompa is -- the Escondida Copper Mine. Mosses also have alternation of generations and a beautiful but somewhat less eclectic selection of reproductive structures, but I will save that discussion for another day. It's unsurprising to find mosses and liverworts at such a spot on Socompa because mosses and liverworts are what biologists would call "ancestral" -- that is, they more closely resemble the common ancestors of plants than conifers or flowering plants do. They are of a form that is necessarily tied to water, since those ancestral plants had only recently left the oceans. In fact, mosses and liverworts cannot live without flowing water during at least part of their lives, because to make that pointy thing (called a sporophyte -- or spore plant), a sperm has to swim out of the boy-part of the plant through a film of water on the surface of the plant to find the girl part of the plant. How's that for sperm mountaineering? But aside from their need for water, bryophytes are quite hardy. When the first plants sprouted out of the seas, land was probably a forbidding, empty, UV-drenched place. Sound familiar? I'm going out of town today, but next week I'll be back with a look at some other great critters from Socompa.

wiki_deer_tick

Jennifer Frazer — Tue, 28 Jul 2009 21:30:23 +0000

A Tick in the Family Way

Jennifer Frazer — Tue, 28 Jul 2009 21:48:12 +0000

Today is my birthday (woo hoo! I survived another year!). In honor of this feat I will take a break from my Very High Life posts to bring you the touching birthday story of . . . several hundred baby ticks. It all began with a very full mama tick . . . [caption id="attachment_906" align="alignleft" width="612" caption="Not a full tick nor even yet a mama tick. Tick for illustrative purposes only. Do not lick tick. This is Ixodes scapularis -- the deer tick."][/caption] . . . which was plucked off a dog and, rather than being flushed, was stashed in a glass vial in a very simple science experiment we could all conduct at home. I cannot decide whether what happened next was more cool or more gross . . . you decide. With pictures!

The Hungry Amoeba

Jennifer Frazer — Sun, 02 Aug 2009 14:40:29 +0000

Oh, those wily amoebae. I think we've all had days like this at the office. Some sensitive viewers may find this disturbing, although no more disturbing, I suppose, than watching a gazelle get chased down by a cheetah on the Discovery Channel. The poor little guy who gets it in this video is a little ciliate flagellate(single-celled organism with a long propeller-like propulsive tail) named Chilomonas, according to the author of the video Psi Wavefunction (thanks Psi!). This little drama is one example of the billions of such daily struggles that go on every day in the soil and water all around you. With our daily lives so full, it's easy to forget. This process of eating by engulfment is called "endocytosis" by biologists, which is a fancy term for "into the cell". Specifically, this is "phagocytosis", or cellular eating. Many cells can also perform pinocytosis, or cellular drinking, where cells can ingest small bubbles of water. Plasmodial slime molds (oft mentioned and beloved at this blog) start out as single amoebae like this, doing pretty much this the exact same thing in the soil. When they fuse to form a plasmodium, they're feeding the same way -- just at 5 Jillion X.

Lichen, Take Me Away!

Jennifer Frazer — Wed, 05 Aug 2009 03:40:36 +0000

You may think that if you've seen one lichen, you've seen them all. Oh, so not so. Yes, many of them do resemble your common leathery grey-green patches plastered on trees like bark band-aids. But there are so many, many more. If you look around, they are everywhere, and they are gorgeous. Today I bring you a delightful seven-minute video with music showcasing some of the diversity of form and color in lichens, and I hope you will wait until you can take a little 10-minute break to relax and savor it. Lichens are more or less co-ops between fungi and green or blue-green algae, which are photosynthetic microbes. The fungus makes the "house", protects the alga from dessication, and absorbs minerals from the surface it's living on, while the algal cells, sandwiched in between thick fungal layers in a cage of filaments, soak up rays to do the cooking. Because many of the algal species found in lichens can live quite happily on their own, (ever seen otherwise bare-looking tree bark glow green on wet days? That's free living algae) scientists don't actually agree over what the relationship is, exactly, between the fungus and the alga. Has the fungus enslaved the alga, purposely keeping it barefoot and pregnant and locked inside its mycelial kitchen? Or are they best buddies homebrewing lichen compounds (the chemicals that make so many brightly colored) in the lichen frat house? Is the nature of the relationship more or less consistent for all algal species, or does it vary? These are fascinating questions which, to the best of my knowledge, are still not fully answered. I have not forgotton about finishing up the Very High Life series, but life has intervened, and one weekend of busy-ness has turned into three in a row, and on top of that I remodeled my house and am writing a freelance story that is competing for my blog working time. I will not leave you hanging at 17,000 feet forever, I promise. But FYI, I may be posting less frequently and less lengthily for the next week or so.

CDC_marburg_virus_filovirus

Jennifer Frazer — Fri, 07 Aug 2009 13:45:23 +0000

Wiki_Rousettus_egyptiacus_egyptian_fruit_bat

Jennifer Frazer — Fri, 07 Aug 2009 13:48:43 +0000

More Bad News for Bats: Marburg Virus Edition

Jennifer Frazer — Sat, 08 Aug 2009 06:22:57 +0000

[caption id="attachment_957" align="alignnone" width="567" caption="The filaments of the Marburg virus, which can be straight or contain a "shepherd's crook", and which gave the filovirus family its name.This photo of the Marburg virus brought to you by the number 11, the letter d, a backwards Egyptian s, and an important (and suggestive) year in US history with a bubble wand on top. Also, by the CDC and Drs. Erskine Palmer, Russell Regnery, and Hermann Rorschach, who in no way support or endorse my interpretation. Magnification 100,000 x."][/caption] As if the bats of the world didn't already have enough to contend with, what with their bad (albeit sometimes deserved) rap for rabies and drinking human blood, numerical decline thanks to habitat loss, and the White Nose Syndrome that is anihilating the bats of eastern North America (and maybe eventually all of North America), last month came news that a reservoir for the deadly Marburg virus had been confirmed: African cave-dwelling fruit bats. This is big news because scientists have been looking for the natural reservoir species for Marburg and its cousin Ebola for some time. Marburg and Ebola are hemorrhagic fever viruses that are among the deadliest on the planet*. They are sole members of the Filovirus family, and are single-stranded negative-sense RNA viruses. Mortality rates range between a quarter and nine-tenths of those infected. And Marburg is not a pleasant way to go. Here's how the CDC describes it:

After an incubation period of 5-10 days, the onset of the disease is sudden and is marked by fever, chills, headache, and myalgia. Around the fifth day after the onset of symptoms, a maculopapular rash, most prominent on the trunk (chest, back, stomach), may occur. Nausea, vomiting, chest pain, a sore throat, abdominal pain, and diarrhea then may appear. Symptoms become increasingly severe and may include jaundice, inflammation of the pancreas, severe weight loss, delirium, shock, liver failure, and multi-organ dysfunction.

Sounds fun! Hemorrhagic fevers are so called because they somehow punch holes in capillary walls that allow blood to seep into the body and out of certain external openings you would not wish blood to ever pass through. As recounted in Richard Preston's gruesome early 90's bestseller The Hot Zone , this can cause people to spill or spatter infectious blood all over any unfortunate passersby or airline seatmates (sometimes the little "summon stewardess" button can't fully convey the depth of your need). It must be said, however, that the bleeding isn't usually what kills you, and that unlike its cousin Ebola, Marburg is not nearly so inclined to make you bleed from bodily orifices. Whew! In The Hot Zone, Preston described (at least in my memory) how some cases of Marburg or Ebola were found in people who recently visited mines or caves or who had spent times in rooms or factories where bats roosted. Although some people seemed to acquire the virus from sick apes or bushmeat, scientists already suspected the virus reservoir, or full-time host, was not apes or monkeys, because they die just as we do from the virus. Suspiciously, however, apes and monkeys that transmitted the virus had often fed at fruit trees that bats frequented. But repeated tests of bats and the sticking of unfortunate "sentinel species" in caves to see if they got sick could never produce leads. For decades, scientists were baffled and frustrated. How could such a deadly virus remain so mysteriously hidden? Then four years ago a survey of more than a thousand small vertebrates Gabon and Democratic Republic of Congo during an Ebola outbreak turned up evidence of asymptomatic Ebola infection in bats, hinting they might be the long-sought reservoir. Inspired, scientists in 2007 finally isolated antibodies and Marburg virus genetic fragments from fruit bats. Then last month an article in PLoS Pathogens contained the damning evidence: the isolation of live infectious viruses from the Egyptian fruit bat (Rousettus aegyptiacus) in Kitaka Cave, Uganda. There can be little doubt now that bats are carriers. [caption id="attachment_958" align="alignnone" width="600" caption="Could you resist this face? No! Bad bat! Don't give me deadly Marburg Hemorrhagic Fever! The Egyptian Fruit Bat, Rousettus aegpitiacus. Courtesy Dawson, Creative Commons Attribution 2.5 License. "][/caption] The infected bats appeared healthy, and the genetic diversity of the viruses found in Kitaka Cave seems to indicate Marburg has been living with and adapting to the bats for a long time. If the virus had only recently penetrated the bat population from another species, you'd expect there to be only one or a few virus types. Moreover, a significant share of the bats in the surveyed cave are infected. About 5.1% of their sample hosted the virus, which, if extrapolated, would mean over 5,000 bats out of an estimated 100,000 in the cave are infected. And indeed, two miners infected in Kitaka were sickened by different strains of the virus, implying they picked up their diseases independently and that human transmission is not a rare event. The strains, though different, closely matched the sorts of strains found in the scientists' fruit bat samples. Although the viral lineages were highly variable within Kitaka Cave, some strains found in one part of Africa were much more closely related to strains found in caves hundreds of miles away than they were to strains in their bat neighbors. As the bats migrate hundreds of miles and mingle over most of the continent annually, it's not hard to see why Africa may be one giant Marburg virus melting pot. I just hope this news doesn't prompt a bat holocaust in Africa on the part of people, corporations, or authorities. Bats have enough troubles already and [cliche alert] provide valuable ecosystem services[/cliche alert] by hoovering up pesky insects and/or dispersing seeds. The solution, I think, is bat avoidance, though how practical that is in a mine I do not know. Note to self: scratch caving in Africa off to-do list**. ------------------------------------------------------------ *In other news, the first-ever case of Marburg in the United States was recorded in February in Colorado . . . wait, what? A deadly Ebola relative made its way to Colorado this year and I didn't even know it? How they managed to keep the fact that a virus with a 90% mortality rate was in Colorado on the DL I'll never know, although I did find an article in the Rocky (RIP) about it ex post facto. I need to start keeping closer tabs on our local newsgathering establishment. **Several of the people who got sick (including the Colorado victim) did so after visiting some sort of "python cave" in Uganda that also is home to thousands of bats (do the snakes just sit on the ground with their mouths open waiting for manna from heaven?). Second note to self: question sanity if *ever* consider visiting something called a "python cave". "Snakes. . . . why'd it have to be snakes?" "Pythons. Very dangerous. You go first."

Who Are You Calling a Slime Mold?

Jennifer Frazer — Fri, 14 Aug 2009 13:43:48 +0000

[caption id="attachment_996" align="alignleft" width="398" caption="The father of taxonomy, one of my three science heroes, and the inventor of the index card: Carolus Linnaeus. In his buttonhole is his favorite flower, the twinflower, subsequently named Linnea borealis in his honor. Note the powder on his coat from his wig. Painting by Alexander Roslin."][/caption] That which we call a rose by any other name would smell as sweet, claimed Juliet, but could she say the same for a nameless rose? Perhaps not. In case you missed it this week, fellow Cornell alum and science writer Carol Kaesuk Yoon produced a lovely article in the New York Times adapted from her new book on the decline of taxonomy that is well worth your time. Taxonomy -- the science of naming and classifying organisms -- and the study of obscure organisms have been dying long slow deaths, as any taxonomist can tell you. Funding for such projects has often been usurped for molecular, pharmaceutical, or biotechnical work. And of course, these projects are important. But so is taxonomy, and Yoon argues that the discovery and naming of life is a deep-seated biological urge among humans. Cultures everywhere sort living things into the same basic categories and feel the same urge to give them two-part names. Briar rose, it seems, is even sweeter. This urge is apart from any value we might derive from discovering among new organisms new pharmaceuticals or modes of operating a cell that could inspire us medically or biotechnically (and believe me, the number of crazy ways you can operate a cell is mind-boggling. Click on any group here to get an idea). More startlingly, she describes research showing it is possible for people to suffer brain injury that makes them unable to recognize anything living, while remaining perfectly capable of recognizing a toaster or stapler. In my conscious mind, I barely remember that something like a carrot is living at all, it's so far removed from its natural setting. Consciously, I classify it more as food. But people with this disorder cannot look at a carrot and tell you what it is because it is living, regardless of whether you or I or they would consciously think of it that way when naming it. What an amazing finding! Regardless of our difficulty as scientists at deciding on the boundaries of life (see viruses), something deep and innate in human brains does so instantly and unconsciously, and uses it to classify and store new ideas in the index of our minds. If taxonomy has been declining among scientists, it has virtually disappeared among the general public. Tomorrow I'll share a small revelation I had in this regard when I stumbled a few weeks ago upon a 19th-century second grade reading primer.

wiki_carolus_linnaeus

Jennifer Frazer — Fri, 14 Aug 2009 14:15:48 +0000

Second Grade Primer, 1897

Jennifer Frazer — Sat, 15 Aug 2009 17:11:37 +0000

Second Grade Primer, 1897

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The Biology and Taxonomy of a Second Grade Primer, 1897

Jennifer Frazer — Sat, 15 Aug 2009 17:58:05 +0000

In my last post I discussed Carol Yoon's recent article and book on the decline of taxonomy among scientists and the public. Taxonomy, which could easily be a dinner conversation subject and hobby for most of the 19th century (TR had quite extensive collections in his youth, for example), has virtually vanished among the general public today. This was brought to my own attention a few weeks ago, when I discovered a second grade primer published in 1897 on the desk of a colleague who collects old maps. I opened and began skimming. The inside cover announced in spidery childhood cursive that the book had belonged to one Mildred Pennington, of Cuba, Ohio. I looked up Cuba, Ohio on Google Maps and discovered it is nothing but the intersection of a highway with one or two buildings now. The first 16 pages were, unfortunately, missing. Here's the copyright page and the first existing page of the text. The image should be familiar to every American . . .You Know Who is standing in the doorway watching. The engravings that illustrated the text were astoundingly beautiful, and stories were an impressive assortment of "modern" tales, fairy tales, and fables. And there were two stories from ancient times, one set in Rome called "Androclus and the Lion", and another set in Persia, called "Filling a Basket with Water". Here is an engraving from the Persian story. There also seemed to be a fair balance of stories calculated to appeal to either boys or girls. But what struck me even more was the way natural history permeated the book. There was a story about a boy who nursed the broken wing of a bat he named Bobby, and stories on the natural history of bees and butterflies and the beaks of birds. Finally, the elusive snipe is found! And gloriously, On p. 20-22 in the margins were beautiful line engravings and the names of eight different species of oak (scarlet oak on last page not shown). At the end of the story, the text asks the student, "Do you know how many kinds of oaks there are? Find as many kinds of acorns as you can. Find as many kinds of oak leaves as you can. Which kind of oak tree grows the tallest? Which kind bears the largest acorns? Which kind has the smoothest bark?" Remember, this is a reading primer, not a biology or science book. According to Yoon's article, a two-year old child of the Tzetzal Maya people of Mexico can name 30 plants, and a four-year old, 100. How many can you name? At the end of the book is this page. I thought you might like to see it too. And being Victorians, they couldn't help but embellish the back cover as well . . .

wiki_polychaetes

Jennifer Frazer — Sat, 22 Aug 2009 23:21:27 +0000

The Swimming Green Bomb

Jennifer Frazer — Sun, 23 Aug 2009 05:02:26 +0000

UPDATE: Now with fabulous Swima photos courtesy lead scientist Karen Osborn! . . . Is not the name of a new DARPA grant project. All over teh intert00bz this week was the story of a newly discovered group of annelid polychaete worms following the publication of a paper describing them in Science. Remember annelids? Segmented (often) worms? The ones with the "human-like" blood? Like tube worms and sludge worms and . . . oh yes, of course, leeches and earthworms. Let's have a look, courtesy Ed Yong: Ok, well that's pretty cool, but not too much to see here. Built like a trireme, moves like a belly dancer, swims in the deep ocea. . . . holy ****! It's got glowing green sacs of goo on its neck that it launches like floating chinese lanterns when poked! [caption id="attachment_1118" align="aligncenter" width="583" caption="Swima sp. Used with permission courtesy Karen Osborn"][/caption] Wow! According to the scientists who discovered them, the worms are probably using these like submarine countermeasures -- the old lure-the predator-towards-the light while you scuttle quietly away. There are four bomb docking points on either side of the neck (the authors call them "bomb bays" in the paper's supporting material). The worms seem kinda stingy with them, though, and will only release a few at a time if poked. It probably takes them a while to grow back. The authors had the guts to name the genus Swima, and one species Swima bombviridis -- the swimming green bomb. The bomb throwers aren't rare, either. They are large (a few centimeters long), common organisms that are fairly widely distributed, judging by their pads off both the coast of California and the Phillipines. And there are many different sorts. Here's a tree illustrating some relationships between the groups. [caption id="attachment_1119" align="aligncenter" width="480" caption="A proposed family tree for the genus Swima. Note the bodies are transparent except for the gut. Used with permission, courtesy Karen Osborn."][/caption] Inside each bomb are two large and two small compartments that are probably breached when the bomb is ejected to mix chemicals that react to light up the whole sac. At a historic site at Rocky Mountain National Park a few weeks ago I heard about a similar concept in fire extinguisher design from the 1920s. . . break glass to mix chemicals, which react to remove any oxygen, fire, and aerobic life from the room. I'll stick with my red cylindrical pressurized mace, thank you very much. Ah-hem. Polychaetes. Right. These worms are polychaetes, which means, roughly, many bristles. The bristles (called setae) are made of a very interesting polysaccharide called chitin, which is found, strangely enough, in hard invertebrate body parts and the cell walls of fungi. Setae extend from parapodia, or foot-like projections from each segment. The parapodia are rife with blood vessels that help the animal exchange oxygen for carbon dioxide. [caption id="attachment_1105" align="alignleft" width="342" caption="On the left, a trochophore larva. "One day I will be a beeee-utiful chiton". Center, metamorphosis. At right, a juvenile."][/caption] And polychaetes have a very interesting ciliated larval form called a trochophore; that is, they have lots of little filaments that beat back and forth to move it around. Annelids aren't the only group that has trochophores; mollusks and a few others do too. If you saw one floating in the ocean on its own, you might think it was a protist, or single-celled microbe (hmmm. . . . ). In order to get a big polychaete, the trochophore starts adding segments, and presto chango, you have annelid worm! Above is a picture of the general process for a chiton, a kind of mollusk. [caption id="attachment_1085" align="alignright" width="467" caption="The variety of known polychaetes, ca. 1800s. I love these 19th century biodiversity prints. Question: Why are they all by Germans? "Borstenwurmer des Meeres". A variety of marine worms. In: "Das Meer" by Matthias Jacob Schleiden, 1804-1881. P. 446. Library Call Number QH91.S23 1888. Image ID: libr0409, Treasures of the NOAA Library Collection"][/caption] There are some 10,000 known polychaete species in a variety of hallucinatory flavors. Some are free-swimming, like Swima, while others live in tubes or burrows. Many are brightly colored, like christmas tree worms, fan worms, and peacock worms. You can get an idea of the cutting edge knowledge of polychaete diversity (ca. 19th century) from the print at right. Only the freshest and most up-to-the-minute science for you, dear readers. Yet it is assuredly, despite its intriguing diversity, miserably outdated. We didn't even know that this major, distinctive polychaete group existed until one swam in front of a submersible in 2001. What else don't we know about? For a nice slide show of various Swima species, check out this gallery by National Geographic.

Wiki_Polyplacophora_ontogeny_trochophore

Jennifer Frazer — Sun, 23 Aug 2009 13:29:24 +0000

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Jennifer Frazer — Tue, 25 Aug 2009 02:18:42 +0000

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Jennifer Frazer — Tue, 25 Aug 2009 02:21:10 +0000

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Jennifer Frazer — Tue, 25 Aug 2009 02:33:53 +0000

Have You Seen This Creature?

Jennifer Frazer — Wed, 26 Aug 2009 03:30:01 +0000

'Cause scientists sure haven't. And they really, really want to. The creature in question is Paleodictyon nodosum. And before you do anything else, go check out this article in the New York Times by William J. Broad and take a gander at it. If this is a blog about the weird wonderfulness of life on Earth, I don't know how something could qualify more. Whatever this is, it is very weird, and it is very wonderful. [caption id="attachment_1125" align="alignnone" width="567" caption="The sort of habitat our mystery creature lives in, and the submersible that has tried to find it. DSV Alvin sets a lander basket with tube cores on the bottom. Note the encroaching darkness. Think of yourself living in that environment -- a soft mud bottom, and nothing but miles and miles of cold, inky blackness, as far as the eye can't see. Credit: National Oceanic and Atmospheric Administration/Department of Commerce"][/caption] There are a few creatures on Earth we knew as fossils before we met face to face. Take the coelacanth. Scientists were shocked to discover a very much alive specimen of this be-lobe-finned fish hauled from the depths off South Africa in 1938. Prior to the discovery of this bit of rather irrefutable evidence, scientists believed the fish went the way of the dinosaurs (literally) at the end of the Cretaceous, 65 million years prior. Although not the first, Paleodictyon is probably the only member of this fossils-first group that was briefly considered to be evidence of some sort of alien deep sea race (hellooooo, Abyss) before it was connected to its fossil ancestors, essentially unchanged after 500 million years. According to the article, scientists have suggested the hexagonal tubes they have found may be bacteria farms, worm burrows (or both), or the trace fossils of decayed compressed sponges that have long ago been scavanged. The paper even suggests such a sponge may have ties to the Ediacaran fauna, a class of bizarre creatures that preceeded the Cambrian Explosion. There's one other candidate for Paleodictyon's identiy: a xenophyophore. They are the subject for another blog post, but the short, short version is that they're gigantic single-celled organisms big enough to fit in the palm of your hand, which (like slime molds!) are multinucleate and feed by engulfment using pseudopodia, and (unlike slime molds) inhabit casings they put together with odd things lying around, including (sometimes) their own feces. In spite of being startlingly obscure, these things are apparently quite abundant on certain parts of the ocean floor. Still, this possibility doesn't quite seem to fit the bill as no xenophyophore crunchy bits have ever been found in the hexagonal holes. What about you, readers? What do you think Paleodictyon nodosum is? If you think you know the answer, write it on the side of a Deep Flight Super Falcon High Performance Winged Submersible with carbon fiber pressure hull, dual cockpit flight controls, heads-up instrumentation, and laser "collision avoidance feeler beams", and mail it to Jennifer Frazer, General Delivery, Boulder, CO 80301. Or put it in the comments below (boooo-ring!). Creative answers encouraged!

Two Sides to Every Worm: the Polychaete Nereis

Jennifer Frazer — Sat, 29 Aug 2009 15:11:51 +0000

In honor of our foray into the world of polychaete worms this week, I thought I'd share some closeups of a polychaete that has been the subject of many an invertebrate lab dissection: Nereis. In this first video you can see our subject looking kind of cute and shy (awwww!). Pay attention to the dorsal (top) vessel and you'll see the "human-like blood" being pumped through the worm's closed circulatory system (just like us!). In Nereis, the dorsal vessel itself does most of the pumping. Also note double eye spots (this guy is literally a four-eyes) and the leg-like parapodia with their bristly setae. But in this video you'll find Nereis has a second, distinctly not cute side: vicious predator. Watch for it to evert its pharynx, and particularly watch for the TWO GIANT FANGS (technical term: jaws) on the end. You can also see the pumping blood at the beginning of this film. Unfortunately, this one is a bit dark. Although you may be tempted to think these guys are closely related to millipedes and centipedes, they're not. This is yet another case of -- you guessed it -- convergent evolution.

Gone Slime Mold Huntin'

Jennifer Frazer — Sun, 30 Aug 2009 13:26:31 +0000

In yet another sign of what an incredibly big dork I am, I have arranged to go slime mold collecting with Rocky Mountain National Park's volunteer slime mold expert. We will be going to an undisclosed mountainous location well outside the park. I am bringing my shockingly inadequate camera but if I find anything worth sharing, I will definitely post it here later this week! I need hardly add that it is still bolete and chanterelle season, so with any luck, I will have something for both brain and table. Happy Sunday . . .

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Jennifer Frazer — Tue, 01 Sep 2009 02:59:05 +0000

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Jennifer Frazer — Tue, 01 Sep 2009 03:00:12 +0000

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Jennifer Frazer — Thu, 03 Sep 2009 01:43:29 +0000

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Jennifer Frazer — Thu, 03 Sep 2009 01:49:24 +0000

Slime: Check. Mold: Check. Slime Mold: Not So Check. Some Wet Colorado Crannies in a Dry Late August, Part I

Jennifer Frazer — Thu, 03 Sep 2009 03:12:38 +0000

[caption id="attachment_1178" align="alignnone" width="500" caption="Not what you're thinking, I swear . . . Photo courtesy Mary Jane Howell."][/caption] Well, the big slime hunters (slime mold expert Mary Jane Howell and I) have returned from our foray but, alas! without many slime molds. Nonetheless it was a day well spent, full of fluttering green aspen, mossy corners, and bubbling pools. We crawled our way into the moistest, juiciest spots we could find, but unfortunately, in August in Colorado in a year without a proper monsoon (as our traditional early August rains are known), it's crispy out there. The bogs are boggy and buggy, but the logs are dry on top and the slime spores have flown. What you see in the picture above is not a slime mold. It is a jelly fungus, called so because of its appearance and slick, rubbery texture. If you ever see one of these, feel free to reach down and pet it -- they feel delightful and do not bite or sting. Jelly fungi are basidiomycetes like mushrooms. That means they make their spores on the outside of special reproductive cells called basidia (singular: basidium). Then there was this: [caption id="attachment_1189" align="alignnone" width="500" caption="A pincushion? A voodoo mushroom? A balding mushroom that decided to get "plugs"? Photo courtesy Mary Jane Howell."][/caption] Super cool! This is an LBM (little brown mushroom) of some sort that seems to be getting parasitized by a zygomycete (like Rhizopus stolonifer, the common bread mold). Zygomycetes in the order Mucorales have a characteristic asexual spore structure (a sporangium) that often looks like a black ball at the end of a long filament, as you see here. There were several mushrooms in the group that had fallen prey, and a few that so far had escaped. Up next time: More slimy, rusty, and snaily goodness from the woods of Colorado.

Slime Mold Hunt Aug 2009 006

Jennifer Frazer — Sat, 05 Sep 2009 13:26:14 +0000

Slime Mold Hunt Aug 2009 006

Jennifer Frazer — Sat, 05 Sep 2009 14:09:40 +0000

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Jennifer Frazer — Sat, 05 Sep 2009 14:20:48 +0000

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Jennifer Frazer — Sat, 05 Sep 2009 14:29:38 +0000

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Jennifer Frazer — Sat, 05 Sep 2009 14:38:29 +0000

Rusty Summer: Some Wet Colorado Crannies in a Dry Late August, Part II

Jennifer Frazer — Sat, 05 Sep 2009 14:47:19 +0000

When I was young, I used to think that leaves just naturally got spotty and brown as they aged. But after taking plant pathology, I learned those spots you seen on leaves are almost always fungi or insects infesting plants, and careful examination with a hand lens can reveal a whole new little world to you. As we walked through the woods last week, I saw many leaves with yellowing spots on top. I turned them over, and lo, underneath were creamsicle-orange piles of rust spores. Rusts are one of the oldest known plant pathogens, and the Romans even had a god –Robigus — dedicated to staving off the stuff (and that included the rust of metal — not having microscopes, Romans considered them one in the same). Rusts are fungi that go through incredible reproductive gymnastics, producing up to five seqeuential spore types in five different reproductive structures and jumping among two or three different hosts per life cycle. I think the rusts are abundant this year because we had such a wet June in Colorado, but that is just a guess. Heavy infestations hurt plants, but in the woods they are very pretty to see if you turn over leaves to see the eponymous rusty-orange urediospores underneath. Mycologists have long, difficult-to-pronounce names for each rust spore type and spore-making body (naturally), but we’ll save those for another post. Just like our jelly fungi and zygomated mushroom, rusts are basidiomycetes, one of the four major groups of fungi. The others, for reference, are chytridiomycetes, zygomycetes (as we saw last time), and ascomycetes. Ascomycetes are fungi that make their spores inside sacks called asci (yes, pronounced ass-eye (singular ascus: ask-us). My plant path grad school department once had a soccer team named after asci that grow without an enclosing structure: "The Naked Asci"), and we found several of these on wet wood too. Many, but by no means all, come in cup form. Eyelash cups (Scutellinia scutellata), in particular, peppered many waterlogged branches with their lashed but lidless eyes. [caption id="attachment_1255" align="alignnone" width="611" caption="A body double for our Molly eye-winkers -- I forgot to get a picture. Image courtesy Dan Molter, Creative Commons 3.0 Attribution-ShareAlike 3.0 license. Click image for link."][/caption] Next time: Slime molds. I promise. Also snails. Cute snails. You know you can't resist.

wiki_scutellinia_scutellata

Jennifer Frazer — Sat, 05 Sep 2009 15:00:34 +0000

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Jennifer Frazer — Tue, 08 Sep 2009 13:34:02 +0000

Slime Mold Hunt Aug 2009 001

Jennifer Frazer — Tue, 08 Sep 2009 13:44:36 +0000

Finally, the Slimes! Some Wet Colorado Crannies in a Dry Late August, Part III

Jennifer Frazer — Tue, 08 Sep 2009 13:50:35 +0000

[caption id="attachment_1234" align="alignnone" width="500" caption="Slime mold sporangia (spore capsules) broken open and laid bare to the wind as nature intended. A few unopened capsules are on the left. Photo courtesy Mary Jane Howell."][/caption] At last, two actual slime molds! As hard as I searched, the best I could find were plenty of tiny white-spored objects (fungi) erupting from the wood. I learned slime mold spores tend not to be white. : ( But local slime mold expert Mary Jane Howell's sharp eyes picked out two (not so slimy) slimes. One, a Stemonitis, often called "hair growing on wood" because of their long spore-making sacs called sporangia, had lost most of its spores and was fairly unexciting. Only the hairnet-like frame of the sporangium was left, and even that was a bit disarrayed. But another, Perichaena corticalis (top photo), still showed the bottom half of its spherical spore capsules and a thin veneer of yellow spore dust. I also learned there is a certain age of fallen log that is ideal for slimes -- bark starting to come off, but not all off, and that looking underneath the log or bark can also bear fruit. To review, plasmodial slime molds start out as spores that hatch into amoebae or flagellated swimming swarm cells. The amoebae crawl around for a while feeding on bacteria and other microorganisms in the soil until they run into a mate. After they fuse, they eventually start pumping out nuclei and more cytoplasm like crazy but everything stays in one big bag -- the plasmodium -- that crawls around until things dry out. They then produce the fruiting body, of which the spheres of Perichaena above are one form. When those dry out and crack open, the spores are distributed by the wind. Fungi and slime molds aren't the only thing I look for when I'm out. I also pay attention to lichens and plants, which have the indisputable advantage of being much more abundant and much less dependent on recent rain for viewing. I found a new (to me) species of bog or rein orchid (Platanthera sp.), pixie sticks and pixie cups (lichens, probably Cladonia sp.), and everywhere the jewel-like fiery red pendant berries of clasped-leaved twisted-stalk (Streptopus amplexifolius) of the lily family. Lilies are monocots, one of two major flowering plant divisions. These plants tend to have parallel veins and flower parts in threes -- if you click on the link, notice the leaves with parallel veins and 6-petaled (tepaled, actually) flowers hanging from their twisted stalks. Finally, we found, in turning over damp branches, several of these tiny snails. As you can see, they are plenty slimy, and plenty cute. Do we have any invert experts here who can ID them? Here ends the tale of the slime mold hunt!

wiki_cassiopea_jellyfish

Jennifer Frazer — Thu, 10 Sep 2009 03:46:49 +0000

Juxtaposition of Jellyfish

Jennifer Frazer — Fri, 11 Sep 2009 03:13:15 +0000

[caption id="attachment_1279" align="alignnone" width="574" caption=""Come here often?""][/caption] Here in Boulder there is a restaurant that serves the proposterously-named "Juxtaposition of Duck". I could not resist when it came to titling this post. From the Beeb, I present to you a gorgeous eye-candy gallery of Arctic jellyfish. One of my great delights in studying the diversity of life on this planet is the variety of form, texture, and color. Slime molds, lichens, and jellyfish, in particular, provide some of the best highs. Enjoy, and Happy Friday. BTW, is it just me, or does it seem like the caption for #2 should be, "Luke, I am your father!"?

wiki_haeckel_tree_life

Jennifer Frazer — Sun, 13 Sep 2009 20:34:50 +0000

Tree Time

Jennifer Frazer — Wed, 16 Sep 2009 02:21:18 +0000

[caption id="attachment_1302" align="alignnone" width="545" caption="An 1879 tree by Ernst Haeckel with a bit of a bias. The true tree of life is trunkless -- more of a shrub of life, really. There's a root, but no apex. If forced to choose one, personally, my money's on Theobroma cacao. "][/caption] Last time I posted a link to a slide show of beautiful jellies. But I don't want this blog to be only about eye candy. I want to help you learn about new organisms, the often crazy or amazing ways they make their livings, and no less importantly, how they are related and classified. Because I hope to make this blog accessible to all sorts of readers, from precocious 10-year-olds on up, I've struggled with how to help you learn about taxonomy without making you digest the long lists of incomprehensible names found in abundance on most trees. On top of that, I face the problem that classifications are constantly changing.

The Trouble with Trees

Today scientists classify organisms based on how they are related to one another, but unfortunately, it's often quite confusing to figure out. Sometimes comparing one trait -- say, tentacle length -- yields one family tree (often called phylogenetic trees by scientists), and comparing another trait -- say, mean number of biologists devoured attempting to study organism -- yields a conflicting one. Which is correct? Which traits should you give more weight when constructing the tree you think most likely? This is the problem that has launched a thousand theses. Scientists argue about the true relationships constantly, and the trees are rearranged with every publication of a systematics journal. On top of that, once scientists started sequencing the genes of different organisms and making trees by comparing them, traditional taxonomies that had been stable for decades or centuries based on body shape, anatomy, or other observable traits were often upended, leaving things in disarray to this day. And finally, the formal names we give ranks above species like kingdom, phylum, class, order, etc., are largely arbitrary, as is the idea that there are exactly seven ranks. There aren't. The ranks are meaningless as absolute markers, so teaching these names seems to me both confusing and pointless. And yet . . .

The Learning Tree

Some major groups have remained supported by scientific consensus, and other new groups are settling down. And there are true evolutionary relationships among organisms, and themes within lineages of common descent, though individual species can differ radically from their close kin. Learning the major groups helps keep the dizzying diversity of Earth organized in our brains. Strange new species will no longer float around like stray mental post-it notes, but have a taxonomic hook to hang on when you can say . . . ah, that new creature is an annelid. I know exactly which other creatures it's related to. So I'm going to try to start including links to trees with each post. It'll be up to you to explore them as your fancy strikes you. One site I will rely on heavily is the Tree of Life Web Project. Although the descriptions there are often written by scientists for scientists and will be nigh incomprehensible to the lay person, anyone can look at the trees and get a sense of who is related to who and how. Plus pretty pictures help with scary names. : ) Another benefit to studying these trees is seeing how many different organisms are out there that you will never have heard of, and about which so little is known. Virtually every page contains groups that even I -- with six years of higher education in biology and a passion for, shall we say, creative life forms -- have never heard of. So here we go: For jellies and friends, which are contained in a group with the formidable name Cnidaria (ni-DAR-ee-a), you can see the TOL trees here and here and a cuter and more digestible, if less rigorous, tree here. Cnidaria was one of the first animal groups surviving today to split from the rest of the animals -- and it shows.

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Jennifer Frazer — Fri, 18 Sep 2009 03:00:15 +0000

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Jennifer Frazer — Fri, 18 Sep 2009 03:04:05 +0000

Does This Membrane Clash With My RNA?

Jennifer Frazer — Fri, 18 Sep 2009 04:17:10 +0000

[caption id="attachment_1338" align="alignnone" width="567" caption="A membrane, some proteins, and 8 segments of RNA: all there is to influenza. A false color transmission electrion micrograph of the influenza virus. Image courtesy CDC/ Erskine. L. Palmer, Ph.D.; M. L. Martin"][/caption] Until 1933, it was impossible to see a virus. Oh, we knew they were out there. But no one had the faintest clue what they looked like. 1933 marked the year transmission electron microscopy finally achieved resolutions finer than light microscopes were capable of and made it possible to finally glimpse the agents that had mottled tobacco leaves, streaked tulip petals, scarred the faces and bodies of millions, or paralyzed, maimed, and killed millions more. So what's with the doofy colors? Yes, in spite of the awesomely awesome resolution that transmission and scanning electron microscopes provide us with, scientists and alarmist pandemic book cover designers can't seem to resist painting them with gaudy colors (see above). OK, I admit the colors do seem to spice up the images. But this isn't even a case of colorizing something that was colorful to start with -- viruses are quite clear. So what a revelation to see a glass artist team with scientists to produce anatomically correct transparent glass sculptures of viruses and other wee animalcules. That's exactly what British artist Luke Jerram has done, and his creations are truly illuminating. [caption id="attachment_1351" align="alignright" width="370" caption="It's hard to believe, but cashews actually *do* grow on trees. A glass model of Anacardium occidentale, the cashew tree, on display in the Harvard Glass Flower Collection. Model by Leopold and Rudolf Blaschka."][/caption] I must say that his models remind me very much of the intricate glass 19th century models of fungi, invertebrates, and plants I discovered in my college days in dusty corners of Cornell and Harvard, many of which were created by the father and son team of Leopold and Rudolf Blaschka in Dresden, Germany from the 1880s to 1930s. They definitely get my vote for having the C00Lest Jobs EVAR. Intended as teaching aids, they date from a time when color photographs were unheard of and microscopes were a bit primitive. The colored glass models were able to show fine detail far better than either an engraved image or tiny eyepiece could, they did so in 3D, and as the Harvard people like to point out, glass flowers bloom year round. It's nice to see that everything old is new again. Viral family trees

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Jennifer Frazer — Fri, 18 Sep 2009 13:31:18 +0000

When Ostracods Fly and Copepods Fire

Jennifer Frazer — Wed, 23 Sep 2009 03:37:44 +0000

I've been treating myself to the BBC's Blue Planet: The Deep this week, and there are delights in every second of film. One that particularly caught my interest is below. Those of you who recall my post on Swima bombviridis will recognize the same strategy, if not the same artillery, at work here. Now you have to admit -- that orange ostracod is even more amazing than the depth-charge wielding copepod. I mean come on! Had you ever imagined a creature like that could exist? Most ostracods are considerably smaller and are called seed shrimp because of their resemblance to something like a bell pepper seed. The males should get some sort of award for virility; many species have two penises and sperm that can be up to six times the male's body length when fully uncoiled. The ostracod in this film appears to be a female, given the clutch of round objects residing in its posterior. The filmmakers here seem to subscribe to the Star Wars school of foley-artistry: no sound in space? No problem! We'll just give the spaceships cool sounds anyway (good call). Bioluminescence is silent? No problem! We'll just give flashing creatures Super Mario-grade sound effects . . . No offense meant, though, Blue Planet dudes at BBC. I worship your work. Unlike Macgillivray Freeman, who in my opinion have largely squandered the IMAX format with their insultingly stupid and poorly written scripts, in spite of brilliant cinematography . . . Annnnyway . . . .Copepods and Ostracods are actually fairly closely related, both being Crustaceans. Check out the copepod taxon here, but make sure to check out the next highest taxon, Crustacea, to see how copepods and ostracods fit into it. Jumping down the ostracod hole will take you here.

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Jennifer Frazer — Fri, 25 Sep 2009 03:25:29 +0000

The Jelly(nose) Fish

Jennifer Frazer — Fri, 25 Sep 2009 03:40:47 +0000

Because clearly, I can't get enough of all things jelly . . . I spotted this video at National Geographic today. It seems fairly prosaic until the guy starts . . . er. . . palpitating said jellynose. [caption id="attachment_1384" align="alignnone" width="576" caption="Not going to win any beauty contests . . .Ateleopus purpurea. Photo by Rodolfo B. Reyes and Fishbase, distributed under a Creative Commons Noncommercial Attribution 3.0 Unported License"][/caption]

Jellynose fish have cartilaginous bones like sharks, though they are in the same group as bony fishes (Teleosts). They seem to have lost their calcified bones secondarily -- yet another case of convergent evolution. Cartilage is a living connective tissue that pads your joints. In cartilaginous fishes, the stiff, flexible stuff is all the skeleton they have, with one big exception: the teeth. That's why most all we have of those giant Megalodon sharks are their rather imposing choppers (in fact, that's what Megalodon means: mega (huge-***) + odon (tooth)).

As the video says, we know very little about them because they live in the deep sea. Here's a reasonably good hierachy of the group (see right side of page); here you can see how they fit into the Tree of Life web project (look for Ateleopodomorpha).

What do you think that jelly nose is for, other than grossing out "sensitive viewers"? Anyone?

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Jennifer Frazer — Mon, 28 Sep 2009 03:14:49 +0000

The Ladybugs' Block Party

Jennifer Frazer — Mon, 28 Sep 2009 04:29:27 +0000

This weekend I climbed to the top of Green Mountain for the first time. If you are familiar with Boulder, it is the right mountain of the two bearing flatirons visible from town. But the top didn't just contain the usual stunning views. As I neared it, I noticed a few small swarms of lady bugs. Notice the plants on the left. Here's what was on those plants: And as I climbed higher, I steadily saw more. Soon the ladybug population exploded beyond all reason. The air was filled with ladybugs flying to and fro, landing on our packs, clothes, and faces. The orange masses in the following pictures are not orange Xanthoria lichens. They are carpets of ladybugs. This guy clearly cannot believe how many ladybugs he is seeing. Either that, or he is laughing at the lady bugs on the photographer. After consulting the interwebz, it seems what we saw were not native ladybugs, but the Multicolored Asian Lady Beetle, Harmonia axyridis. Unlike our native and presumably sober, upstanding, red-shelled and red-blooded All-American ladybugs, these introduced (from Asia for pest control) guys/gals have multi-colored and variously spotted orange shells. They swarm at the end of summer to find cracks and crevices in which to kick back, order pizza, hook up the cable, and watch 800 hours of the Home & Garden network until spring. Life's rough sometimes. In case you were wondering, it's more proper to call ladybugs "lady beetles" (the scientifically PC term), because true bugs are in the taxon Hemiptera, and our friends are not bugs, but beetles, which form the massive taxon Coleoptera. The most distinguishing character of the beetles are those hard wing covers, known to science by the beautiful name "elytra" (sing. = elytron), which sounds as if it should be the name of a character in a play by Aeschylus. Here you can find the tree containing Coleoptera (the beetles) at the Tree of Life Web Project. To give you a feel for the kinetics of the situation, here's a video of the same event taken above Boulder somewhere at the end of July. Next time you want to terrorize the local aphid population without actually buying a gallon of lady beetles, just show this film in your garden. 5D and EX1 Lady Bug Swarm from Michael Ramsey on Vimeo. And finally, just for kicks, here's the picnic that inspired this "block party" -- a blast from the past for some of us:

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Jennifer Frazer — Wed, 30 Sep 2009 02:41:53 +0000

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Jennifer Frazer — Wed, 30 Sep 2009 02:55:18 +0000

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Jennifer Frazer — Thu, 01 Oct 2009 00:05:27 +0000

Stalking Mushrooms for Science

Jennifer Frazer — Thu, 01 Oct 2009 00:28:01 +0000

[caption id="attachment_1450" align="alignnone" width="614" caption="That lurid orange stripe wasn't visible until vivisection. Neither were the blue maggot holes. Mmmmm. . . maggot holes. Locations redacted to protect the innocent."][/caption] In all the excitement over the ladybugs, I completely forgot to mention I spent the weekend before scouring an undisclosed location for fungi for the 2009 Rocky Mountain National Park Mycoblitz. Citizen science in action! Our Mycoblitz was the brainchild of past Colorado Mycological Society president Rob Hallock (hi Rob!), but it is an example of an increasingly popular endeavor called a "bioblitz". In these events, teams of volunteers and scientists sweep a few select landscapes for one to two days collecting as many organisms of particular groups as they can. They hope to get a snapshot of the biodiversity of a particular place and time. Last year's mycoblitz was (I believe) the first bioblitz ever held in a national park. The picture of me with the very exciting slime mold from my "About" page was taken at that event. This year we purposely chose to do the event a month later -- in September -- to try a capture a different assortment of fruiting fungi. And by all accounts, we succeeded. My team was able to find the first jelly fungus recorded in RMNP and a very special yell0w-staining Ganoderma -- and seven of our 25 specimens found a permanent home in the herbarium in Denver. Here are some more pictures of this year's blitz -- starting with one of some various mycoblitz ne'er do wells. . . : ) One of our two identifiers was Vera Evenson, Curator of the Denver Botanic Gardens Herbarium of Fungi and author of Mushrooms of Colorado and the Southern Rocky Mountains, which I highly recommend to anyone interested in that subject. Vera's hiding in the picture above, examining a specimen very closely. On the left you can also see the food dehydrators we used to preserve all our specimens. Below is the other identifier, Michael Kuo of mushroomexpert.com. Michael is both an English teacher and amateur mycologist who's written the books 100 Edible Mushrooms and Morels. Michael makes me a little embarrassed that I haven't done more with my life. And finally, here's our hearty crew at the campsite in Moraine Park. We were lucky enough to be there during the elk rut, and their beautiful (and sometimes comical) calls were everywhere. A few even wandered into that field in the background and we could see them with our binocs. See what you can experience by volunteering for science? Stunning views! Elk calls! Orange mushrooms! Starlight! Toasted marshmallows! Lots and lots of accession tags! Clothes that smell like smoking logs (and only that if you're lucky!) So keep your eyes and ears open for opportunities. Citizen science is yet another way you can serve your country, make no mistake. At this year's blitz, a retired policeman and schoolteacher who had never done science before saw an ad about the blitz in the newspaper and just decided to show up. They joined my team and found the majority of the specimens that were chosen from our collection to be deposited in the herbarium. So watch for big opportunities like the Christmas Bird Count, or small opportunities like our little mycoblitz. Uncle Sam wants you for science, too. Speaking of Uncle Sam, I will be doing my civic duty this weekend by visiting Washington, DC, for the first time ever. I'll be making my pilgrimage (hopefully) to the Smithsonian, where I may just find some delights to share with you, provided they allow photography. As such, no posts until mid- to late next week. Have a great fall weekend! Get out there and discover some weird stuff in the woods. : )

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Tridented Trilobites and Giant Squid: The Sant Ocean Hall

Jennifer Frazer — Thu, 08 Oct 2009 14:13:50 +0000

[caption id="attachment_1476" align="alignnone" width="614" caption="My old college friend and NIH postdoc Laurie Waters with an actual GIANT SQUID. It wasn't so long ago scientists were still debating whether these actually existed."][/caption] Washington, DC, did not disappoint. The highlight was the Sant Ocean Hall in the Smithsonian Museum of Natural History, newly opened a year ago after a major remodeling of the cross hall it sits in. The hall soars and boasts a life-size whale model; the exhibits beckon with enticing photographs, movies, and a spherical screen on which swirling ocean currents flow across a spinning globe to eerily convincing effect. Welcome to the future. A brief tour of my favorites . . . Above is the super-awesome giant squid, appropriately locked inside a riveted metal case lest it suddenly come back to life, break the glass, and start pillaging and marauding the museum. It was the first time I had seen a specimen in real life, and I must confess that although it was suitably enormous, it seemed smaller (but not shorter) than I expected. That is, of course, easy for me to say as I stand there staring at it from the right side of a riveted glass case, and would, perhaps, be less so were I to encounter one in its natural milieu. As I often say when explaining why I won't hike solo in the backcountry, I'm really quite snackable. The specimen in the case above is the female; the male was smaller and displayed in an ID4-aliens-suspended-in-goo style pose in a case nearby. Very cool, boys. Here's the entrance to the biodiversity display, with perhaps my least favorite part of the exhibit: a boring definition of biodiversity. "Marine biodiversity is the varity of life in the ocean. It is enormously complex. Scientists try to make sense of this diversity by organizing marine organisms according to evoluntionary . . . zzzz" Come on, guys! You can do better than that! How about "Biodiversity is the blizzard of lifeforms that coat the planet with bizarre beauty. It is nematode trapping fungi, slime nets, and nudibranchs that ripple through the water like Spanish dancers. . . " Sigh. Fortunately, the rest of the exhibit made up for this lapse. Although organized a bit confusingly, it was a nice blend of museum specimens, photographs, and strategically chosen videos that startled viewers with short clips of subjects like cephalopods' astounding shapeshifting abilities. Some examples: Laurie again, with the echinoderms. Various worms, including gorgeous polychaete annelid christmas tree worm at upper left. The very cool Ediacaran fossil of Tribrachidium, a pillow-like creature from what is commonly referred to as life's first experiment in multicellularity. This is one of my very favorite organisms ever, and dates from over 550 million years ago. And what a stunning fossil! They had many other famous Ediacaran specimens. And they had crinoids, or sea lillies, galore. I am sorry my photos didn't come out better, because these specimens preserved incredible detail. Many had the architectual gestalt of gothic cathedrals. Here is a better photo from National Geographic. And then there was this fantastic beauty -- I had never seen or heard of anything like this in my life, and I even made it halfway through "Trilobites" by Richard Fortey: There's really only one acronym for this: W. T. F. As you can see in the placard, the Hail Mary Pass of paleontology is "It may have been used for mating." (Props to Laurie for pointing that out. : ) ) No ocean hall is complete without a giant jellyfish. And no visit to Ocean Hall is complete without getting a fuzzy, out of focus shot of oneself with said giant jellyfish. This picture pretty much sums up my feelings on the Sant Ocean Hall, in spite of its relatively minor shortcomings. For another perspective, see this review by the New York Times.

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Jennifer Frazer — Sat, 10 Oct 2009 21:24:49 +0000

Atsa Lotta Sushi: The First Giant Squid on Film

Jennifer Frazer — Sat, 10 Oct 2009 23:04:02 +0000

This is really old news, but since I mentioned it in my last post, I wanted to show you just how recently we finally captured images of live giant squid (Architeuthis dux) . The first still image came only in 2002 after a squid was towed to a harbor in Japan. The first video came in 2006. Here is the original footage as presented on Japanese TV in December 2006. Is that narrator like our movie-trailer guy? It sure seem like he does the voice work for all Japanese newscasts and game shows. When that triumphant music comes on, I imagine he's saying something like, "Congratulations! You caught and filmed a giant squid. You have now leveled up." Here is the National Geographic Society's take on the catch, complete with a better photo. You'll note at 0:35 the squid shoots some water out of its funnel, its "jet engine". Squid fill their mantle (the large upper hood) with water and squeezes it out through this side tube to move forward. Also note that this squid is a young female. As in, it was a mere 24 feet long, and this species can approach 60 feet -- implying it is just 1/3 of maximum estimated size. Why is it incredible we only recently recovered images and film? Scientists have known for over a century that giant squid from the beaks and pieces they dredged out of sperm whale stomachs. Dead specimens had washed up on shores in Newfoundland and New Zealand, from which one lucky specimen even made it to the Rev. Moses Harvey's bathtub. Bathtub technology has advanced considerably since 1873. But because these creatures live in one of the most inacessible habitats on Earth -- the cold, black benthic zone -- live specimens eluded photography (and, for the most part, capture) for another 125 years. The Smithsonian's specimens both came from Spain in 2005, and you can find the details on their capture and display here. Giant squid aren't the only tentacled terrors cruising the depths and hiding from cameras. Though scientists had known since the 1920s about the even larger colossal squid (Mesonychoteuthis hamiltoni) that haunts the treacherous Southern Ocean, the first images, film, and intact collection of this living creature were made only in 2007 by a New Zealand fishing crew longlining for Antarctic toothfish. Colossal squid can reach 46 feet long but have much larger and heavier mantles than giant squid. As worrisome as all I've said so far may be to consider were one, say, out on a pleasure swim at 1,500 meters in squid-infested waters, consider this: not only is the colossal squid considerably larger and bulkier than the giant squid (although its arms are generally shorter), it also possesses hooks on its tentacles. Some swivel. Some have multiple prongs. *Shudder* H.P. Lovecraft, eat your heart out. Squid are cephalopods, which are in turn mollusks. To see a good mollusk family tree, click here. For the technical cephalopod tree, see the Tree of Life Web Project. Not for the faint of heart.

Marine Mucilage: Why They Make Marine Kleenex

Jennifer Frazer — Wed, 14 Oct 2009 04:19:58 +0000

And not to be confused with Marine Muesli. I know you're disappointed. Apparently, in addition to all things jelly, I'm fascinated by all things blobby. You'll note the restraint I used in not posting anything about that blob they found floating off the coast of Alaska last summer. It seemed obvious right from the start that that was simply your run-of-the mill algal bloom. These blobs, on the other hand, would quite mystify me without the help of a reassuring National Geographic narrator. I'm pretty sure this is the same stuff that builds up in the water you leave the dishes in the sink too long. Is it just me or did you also half-expect to see an eyeball or two floating around in one of those things? It seems like this may be some sort of biofilm, which is a very sexy subject in the world of biology right now. Biofilms are essentially thin coats of bacteria and bacterial slime (technically known as extracellular polymeric substance, or EPS) on teeth, stream cobbles, catheters, lawyers, etc. (just kidding lawyers! Don't sue!) These things are apparently everywhere -- even on the thin skin of water at the surface of the ocean -- and this way of life represents an up-till-now severely underappreciated bacterial lifestyle. 99 percent of bacteria may live in biofilms. And yet these don't seem like classic biofilms as they aren't tightly packed or adhered to a surface. They seem to be somewhere in the no-man's-land between a biofilm and marine snow, the slow rain of decaying microbial matter that eventually coats the ocean floor. Both marine snow and mucilages incorporate much more than just bacteria -- like crustaceans, plankton and viruses. For whatever reason the marine snow in the northeastern Mediterranean is piling up faster than the life in the water column or on the sea floor can take it out. Which seems odd, because in the deep sea, the locals will quickly consume anything that isn't ballistic-grade plastic, and I'm pretty sure they have their R&D departments working on that too. Whatever they are, they are unusual, and probably prospering by climate change. I love weird manifestations of life, but there is good-weird and there is bad-weird. The kind of weird that smothers fish and spreads E. coli is definitely bad-weird. For the PLoS paper that inspired this video, click here.

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Jennifer Frazer — Sun, 18 Oct 2009 21:08:27 +0000

When Plesiosaurs Ruled the Sea

Jennifer Frazer — Tue, 20 Oct 2009 03:43:06 +0000

[caption id="attachment_1629" align="alignnone" width="560" caption="Our heroine . . . Dolichorhynchops . . . and her droogs."][/caption] Some life is weird by virtue of time delay. If the inhabitants of the Cretaceous Seaway -- the long strip of semi-shallow ocean that flooded middle North America some 82 million years ago -- could see the vast blubbery mammals that inhabit the seas today, they would no doubt think them odd. And tasty. But it so happens we live now, not 82 million years ago, and it is we that them them odd. You see, in that time, the oceans were filled not with mammals who put out to sea, but with reptiles who did. Large reptiles. With nasty big pointy teeth. The niche presently occupied by dolphins was occupied by icthyosaurs (although they had gone extinct by 90 million years ago) and small plesiosaurs like the four-finned marine reptile Dolichorhynchops (Do-li-ko-rin'-kops), the Lambda-class shuttle of the Cretaceous Seaway. That of the Loch Ness Monster was occupied by long-necked plesiosaurs. And the niche occupied by sharks was occupied by mosasaurs and . . . well. . . sharks. Growing up, I was curious about these mysterious seas and the creatures that inhabited them. But I only had a dim idea of what they were like because the only places to find them were line drawings in books or bones in museums, where they generally took a big backseat to media-darling dinosaurs. Because, and this is a big point to remember, folks – especially if you're talking to paleontologists – these sea creatures are not dinosaurs. Not Dinosaurs. Remember that. In my college dinosaurs textbook ("Dinosaurs: The Textbook"), one of only two places pleiosaurs show up is in the section on ancient reptiles that are not dinosaurs. Dinosaurs, according to "Dinosaurs: The Textbook", can be most easily thought of as a group of extinct reptiles having an upright (not sprawling or swimming) posture. Paleontologists seem quite sensitive on this point. Enter Sea Monsters: A Prehistoric Adventure -- the latest (first?) offering by National Geographic in the world of gargantuan IMAX films. It seeks to fill in this Cretaceous-Seaway-sized gap in our collective imagination. To see the trailer for "Sea Monsters: A Prehistoric Adventure", click here. I saw this at the Denver Museum of Nature and Science two weeks ago at a special screening with a lecture on the science behind the film by paleontologist Ken Carpenter. A Dolichorhynchops is the heroine of the film, but the directors couldn't resist shortening her name to the overly-cute “Dolly”( Can't we just say Dolichorhynchops? Please? Is it really that much harder to say than Dmitri Medvedev or Boutros Boutros-Ghali?). The directors worked with Carpenter to develop the most scientifically accurate reconstructions of these creatures possible. And wow, what a wonderful job they did. Though the plot is a bit treacly (hence the moniker "Cretaceous Bambi" bestowed on the film by Carpenter at the end of my screening), the animations are stunning. Though assuredly, there are gratuitous eye-candy shots of the giant predatory mosasaur Tylosaurus leaping in slow-mo toward the viewer for the benefit of the 3D patrons, they also made sure to include some ostensibly less-glamorous creatures. A mating swarm of glowing red ammonites, for instance. And they used an absolutely fantastic “time lapse” device to illustrate the incomprehensibly vast sweep of geologic time. Carpenter explained that the filmmakers took pains to vet every detail, behavior and design to make sure they were realistic as possible. He'd circle errors and write in corrections on stills. He'd endure marathon hours-long phone-call editing sessions. The directors even persuaded a husband and wife team of professional swimmers to latch on to one another and don plesiosaur flippers to test how a creature like Dolichorhynchops with four fixed fins might have used them in practice. They quickly found they must beat together to get anywhere, and the animators found while working with their computer models that the fins couldn't flip up – a detail that paleontologists had missed until the animators pointed it out. The human parts of the plot are, however, far less successful than the reconstructed animals. Poor acting. Poor scripting. I cringed. At one point, a fossil is being “excavated” by some paleontologists -- but you can clearly see the outlines of the fake fossil cast they apparently plonked in the ground to stand in for a real fossil. But far worse than that were the scripted "scientist" scenes, which I hated the for all the same reasons I hate Macgillivray-Freeman films: cheesy, fakey dialogue and acting and totally unrealistic depictions of scientists. The lead female scientist was particularly unbelievable, inauthentic, smug and annoying. I have worked with women scientists. I know women scientists. Women scientists are friends of mine. Madam, you're no woman scientist. In short, she falls victim to the Elizabeth Shue effect. Ever see "The Saint"? The last decent Val Kilmer movie in which he plays a man of many disguises who falls for the impossibly beautiful, but completely unconvincing physicist? It's not that some female scientists aren't beautiful -- see Lisa Randall. But when directors hire gorgeous actresses to play brainy scientists, the results are usually not good (exception: Jodi Foster). I mean, come on -- how many female scientists do you know that look perfectly coifed and attired with a chic haircut and perfect make-up to go digging in the dirt of backwater Kansas? Couldn't we film some real scientists on a dig for some relevant fossils rather than relying on fake scientists with even faker dialogue? In my opinion, it isn't fair to kids to misrepresent science this way. They're trying to turn them on to science, and to my adult brain at least, the result is both misleading and a turn-off. For a film that took such pains with getting even the tiniest angle of a fin on a fish in the background just right, why couldn't they take such pains with the depiction of science and scientists? Still, the movie works more often than not and it captures a world whose story has gone untold far too long. At one point, “Dolly” barely escapes death by shark, but she doesn't escape having a back flipper nipped and permanently tucked. And sure enough, as Carpenter showed us in his slide show, scientists have actually found a fossil Dolichorhynchops flipper with its back edge missing a shark-bite sized piece. Just don't forget Lesson #1. One of the very first slides in Carpenter's presentation was a dinosaur with a big red circle with a line through it. He took questions after the film, and an audience member asked something about the dinosaurs in the movie. Carpenter looked as though he'd just been hit by a sniper. “Oooooh . . . " he winced. "NOT dinosaurs.” To see if the film is playing in your area, click here.

The Bloodbelly Comb Jelly's Bad*** Soundtrack

Jennifer Frazer — Sat, 24 Oct 2009 18:42:12 +0000

Don't you wish you had an ubercool espionage movie soundtrack to accompany you wherever you go? I know I do. Make sure to hit the HQ button if you have the bandwidth. Actually, I quite wish they'd present more nature videos this way. Do these jellies not have the feel of sleek hyper-space cruisers in this short film? It befits the coolness I think these organisms have, rather than the hysterical watch-me-nearly-die antics and 4th-grade scripting approach (Top 10 most venomous animals!) which many popular modern animal shows lure viewers (A favorite card game of mine parodies one particularly popular version as "The Animal Bothering Show"). These images were captured by a remote rover operated by the Monterey Bay Aquarium, where presumably one very cool member of the staff thought to include the soundtrack. Anyone know where it's really from? So let's talk about this particularly cool creature, Lampocteis cruentiventer. Their stomachs are always blood red; their bodies may come in various shades of the color. They can grow up to about 6 inches long -- about the size of a hand -- and they swim from about 1,000 to 3,300 feet down. That's pretty deep, but not abyssal. Still, they probably never see much of the light of day. Which, strangely enough, explains their brilliant red coloring. Red light is filtered most efficiently by water, and after traveling a few hundred feet down, there is very little left. Thus organisms that are red will appear gray or black in the deep, like a hole in the water. Thus, many deep sea creatures, when illuminated by explorers' lights, appear lurid red. Now let's say, for the sake of argument, you live in the dark and like to eat things that glow. But dang it, you're transparent! Now breakfast is causing you a bit of a problem that cannot be solved by Rolaids. Solution: encase your stomach in the undersea version of air raid curtains -- red pigment. Hence the bloodbelly. (Although it does sound a bit like a better name for a grizzled jazz musician: "Good Evening, Ladies and Gentlemen. My name is Blood Belly and tonight I'm going to play a little number for you I like to call . . . ") Comb jellies are ctenophores ("ten'-o-fours"), which have eight cilia-bearing (small beating filaments) combs called ctenes with which they weakly swim. Whenever I have been lucky enough to visit an aquarium, I have spent many long minutes fogging up the glass staring at the undulating cilia of comb jellies. It's a fascinating riot of colors and textures. The cilia make these the largest creatures to swim by such a mechanism, and give them a superficial resemblance to overgrown Paramecia. Both jellyfish and ctenophores have two cell layers separated by a gooey center, the mesogloea (mes-o-glee-a). This is a chief way they differ from us "higher" animals, who have a fancy middle layer we've parleyed into stomachs, livers, brains, gall bladders, spleens, appendices, giblets etc. Go us! Comb jellies can also have two long tentacles. Instead of the famous stinging nematocysts that true jellyfish bear on their tentacles, comb jellies have sticky cells called colloblasts that rupture to release glue that captures their prey. They then retract the tentacles to bring their food to their mouths. Unlike jellyfish, which have a single opening to serve as mouth and anus (thank GOD evolution didn't stick with that particular system in vertebrates), ctenophores have one opening at the mouth and two at the back, though all three may serve when nature calls. Scientists, as with most groups, are fighting constantly about how cnidarians(jellyfish, corals, and friends), ctenophores, and every animal more complex (usually referred to as a group called "Bilateria", all the mirror-image symmetry animals) are related. As it's a fight that's enormously complicated and still ongoing, I will spare you the details. Suffice it to say, they ARE related. Here is one possible family tree. One final note -- ctenophores are also clearly an inspiration for the creatures in the 1989 movie "The Abyss", a sci-fi classic you should see if you have not (though many in the know urge finding the director's cut). A personal favorite. See here and here for some striking examples. Discovered via Deep Sea News.

wiki_Kronosaurus

Jennifer Frazer — Sat, 31 Oct 2009 02:56:56 +0000

wiki_Spitsbergen

Jennifer Frazer — Sat, 31 Oct 2009 05:06:28 +0000

The Other Expired Marine Monsters

Jennifer Frazer — Sat, 31 Oct 2009 05:35:22 +0000

There's been news on the giant marine predators front. Now, don't get me wrong, they're still extinct and all (I know, I know). But . . . [caption id="attachment_1722" align="alignnone" width="614" caption="The pliosaur Kronosaurus. Still NOT a dinosaur."][/caption] ... this week New Scientist's cover story took a closer look at the four major taxa of marine reptiles, in all their incarnations from the Permian to the Big Cretaceous Sleep. I covered two of them in my post on "Sea Monsters" -- the plesiosaurs and the mosasaurs -- but there are two others: the icthyosaurs and the pliosaurs. You should definitely have a look. And scientists announced this week that they had found the skull of a giant pliosaur in the UK that could have measured 16 meters (52 feet) long – only two meters shorter than the current pliosaur record-holder, a Pliosaurus found in Oxfordshire, UK, that was so big you could fit your arm in its tooth sockets. [caption id="attachment_1726" align="alignleft" width="329" caption="Able I was ere I saw Svalbard."][/caption] New pliosaur specimens have been popping up all over recently. They come from Mexico, the UK, and the island of Spitsbergen in the Hoth-like waste of the Norwegian Svalbard archipelago, which is apparently bursting with pliosaur brittle (thousands of skeletons are presently weathering out in the choice spot). Two massive pliosaur specimens (est. length 15 m.) were excavated recently there and dubbed (in King-Kong-worthy choices) "The Monster" and "Predator X". The icthyosaurs(fish-lizards) -- which resembled dolphins even more strongly than the short-necked plesiosaurs -- were dominant marine reptiles in the Triassic and early Jurassic. Some small species had freakishly large frisbee-sized eyes (for reasons revealed in the NS article). But some had bodies to match -- and this is relatively recent news too. It was only in 2004 that an icthyosaur -- Shonisaurus -- the size of a fin whale (the second-largest living animal) was found in British Columbia. Why were neither of these creatures in "Sea Monsters"? The icthyosaurs died out for unknown reasons by the time "Sea Monsters" was. . . er . . . "filmed". So had the largest pliosaurs. The New Scientist article also features a difficult to find but stunningly informative and useful family tree and size comparison chart for the four groups. Make sure to blow that puppy up so you can actually read it. One final note . . bear in mind that the animals in the New Scientist tree (and our current maximum size estimates for particular groups) represent what we know based only on the fossils we've happened to find. There may have been many more varieties of huge marine reptiles in these four groups -- or maybe another major group – and any of them could be larger or weirder than we've ever imagined. Good specimens may never have fossilized properly, purely by chance. The fossils may be buried in rock layers that aren't currently much exposed at the surface, and are waiting miles underground to be exposed thousands or millions of years hence (or never). Or long ago they may have weathered out and eroded back into the sea whence they came or been sucked down into the mantle and obliterated. Odds are we are seeing only a slim fraction of what once existed. And that is true for all life, especially in the squishy-little-creature category of which I'm such a fan. Biologists, perhaps even more than historians, have reason to lament our inability to time travel. Oh, what wonders we might see if we could. The fossil record, with all its glorious variety, is the merest hint of the splendor that really was, that really happened, and that we will never, never know.

pollen_SEM

Jennifer Frazer — Sat, 31 Oct 2009 14:55:29 +0000

A Trip Down the Microbial Rabbit Hole

Jennifer Frazer — Sat, 31 Oct 2009 22:31:20 +0000

"Where the telescope ends, the microscope begins. Which of the two has the grander view?" – Victor Hugo I think you all know how I would answer that question. [caption id="attachment_1762" align="alignnone" width="614" caption="Pollen from sunflower, morning glory, hollyhock, lily, primrose, and castor bean plants. 500X magnification; the bean-shaped pollen grain at lower left if 50 micrometers (μm) long. Believe it or not, these microbes are actually an entire plant -- the male gametophyte."][/caption] This blog is all about the variety of life, but part of that variety are the enormously different scales at which life can exist. You may know blue whales are the largest animals (ever, actually. Ever.), but they are not the largest organisms. Trees (aspen are notorious for this -- one called Pando in Utah in paticular), fungi (remember the humongous fungus?), and perhaps a mediterranean sea grass called Posidonia oceanica can grow to many square kilometers courtesy their ability to grow asexually and keep at it for thousands of years. Life exists in a contiuum from these titans all the way down to the tiniest bacteria and archaea, the smallest of which are in the 200-400 nanometer range, round about the size of the measles virus. Now the University of Utah has created an animation with a simple slider bar that takes you from coffee bean to carbon atom and back again. Check it out! Notice, for example, the amoeba (yay! Our site mascot!) approaches the size of the grain of salt and is visible to the naked eye when the animation is zoomed all the way out. If I were a bacterium or yeast cell, I'd cower too! Notice also that mitochondria, the descendants of bacteria engulfed by ancestral eukaryotic cells (all cells except bacteria and archaea) billions of years ago, are actually slightly bigger than, but still more or less the same size as, E. coli. Notice that measles virus next to it -- which gives the scale for the tiniest known cells mentioned above. Zoom in and out to compare this to the size of the amoeba or paramecium, and think about the fact they are both what we call "single-celled organisms". Yet if the biggest amoeba or smallest bacterium had eyes, they probably wouldn't be able to see each other. They are an order of magnitude (1000 times) different in size -- and the difference is 10 times the difference between blue whales and us! Don't miss the question at the bottom either, which shows what amazing packers you boys are. A sample:

How can an X chromosome be nearly as big as the head of the sperm cell?

No, this isn’t a mistake. First, there’s less DNA (half as much, actually --jf) in a sperm cell than there is in a non-reproductive cell such as a skin cell. Second, the DNA in a sperm cell is super-condensed and compacted into a highly dense form. Third, the head of a sperm cell is almost all nucleus. Most of the cytoplasm has been squeezed out in order to make the sperm an efficient torpedo-like swimming machine.

Why do I get the feeling that last sentence will inordinately please the gentlemen out there? : )

cdc_aspergillus

Jennifer Frazer — Wed, 04 Nov 2009 04:32:30 +0000

The Softer Side of Aspergillus

Jennifer Frazer — Wed, 04 Nov 2009 14:01:17 +0000

From the Department of More Cool Natural History Videos with Interesting Music, I give you the sexy CGI version of the fungus Aspergillus (ass-per-jill'-us) courtesy of some fine folks in Mother Russia. You may think of this fungus (if you think of it at all) as the scary black bane of your tupperware contents. But in reality, the graceful, proud forests of Aspergillus in your leftover gardens have a softer, more new age side (although they do seem to enjoy bashing into each other . . .)

Almost as exciting as the dinosaurs in Jurassic Park! It's only a matter of time until one of those hyphae (hi-fee, fungal filaments) figures out how to unscrew the lid on its moldy pickle jar. Actually, gratuitous spore bashing aside, this really is a fine animation. What you are seeing are Aspergillus conidiophores, or asexual spore-bearing stalks. As they grow up, spores grow in long chains at the swollen tip of the conidiophore. Although this animation's depiction of multiplying conidia (asexual spores) isn't quite right in the details (if you look carefully, some of those conidia literally appear out of thin air), it's a worthy fakery job. You get the idea. Aspergillus is a very common mold. Odds are its spores are floating around in the room you are sitting in right now, and this video amply demonstrates why. When I was at MIT, I did my thesis on the mold hysteria that gripped the U.S. about 10 years ago. I was flabbergasted by people who seemed to think any mold in the air was cause for panic. The opening line of my thesis was, "Living creatures float in every breath we take." That is situation normal, and has been for several hundred million years. Though you are likely inhaling dozens or hundreds of fungal spores as you read this, healthy immune systems are more than equipped to handle it. In college microbiology lab, Aspergillus was also one of the two fungi we examined in the 10 minutes we weren't coaxing bacteria into pure culture (mostly) or playing with protists (rarely, unfortunately). If you have a microscope (you do, don't you? Oh wait. I don't either. Must work on that.), try scraping some mold off the nearest refrigerator-aged cheese and see if you luck into one of these. Even if not, you might be amazed by what you find. Wee animalcules aren't the only thing worth gazing upon at 100X. Not by a longshot.

: Conidia and conidiophore (fancy science-nerd name for asexual spores and the stalk that makes them) of Aspergillus fumigatus, courtesy CDC.

Fungi have an überweird classification scheme I will tell you about some other time, but suffice it to say it's based on the sexual phases of fungi, and Aspergillus ain't it. However, when the sexual forms are known for Aspergillus species (and they aren't always!), they are placed in the Ascomycota, or sac-forming fungi, which I have discussed before. Here's a tree. Discovered courtesy MycoRant.

wiki_Cetacea

Jennifer Frazer — Mon, 09 Nov 2009 01:19:56 +0000

A Picture is Worth a Thousand Krill per Cubic Meter

Jennifer Frazer — Mon, 09 Nov 2009 01:50:26 +0000

This past month has brought two beautiful whale details to my attention. First, a sperm whale (no. 4, above) was photographed with an actual ginormous chunk of giant squid hanging out of its mouth. Finally! Visual confirmation that all those epic squid-on-whale battles we've long suspected actually do take place. It appeared a Momma Whale was using said piece as a visual aid to teach Baby Whale about the merits of deep diving for food. National Geographic had a nice photo gallery of the event. And second, a blue whale (no. 6) killed by a benthic mapping vessel washed ashore in northern California, providing both a sad example of one of the big threats to whales (ship collisions) but also an A+ opportunity to take some blue whale blubber and tissue samples. And it provided a light bulb moment for me in the form of this stunning photo. Blue whales are actually blue! And what a beautiful blue too. Who knew? I always figured it was figurative, like the "right" in right whales (no. 3; they were easy to kill, so they were the "right" whales to whalers) or the sperm in sperm whales (whalers mistook their spermaceti for actual sperm). Water appears blue . . . the whales look blue under water . . . hence blue whales, right? Wrong. Thanks to Reed Esau for drawing my attention to the sperm whale/squid hunting lesson.

Wiki_Chrysaora_quinquecirrha

Jennifer Frazer — Wed, 11 Nov 2009 03:47:29 +0000

Life on Earth Has a Soundtrack?

Jennifer Frazer — Wed, 11 Nov 2009 04:21:19 +0000

[caption id="attachment_1844" align="alignleft" width="398" caption="Why do I suddenly feel . . . melancholy? Image by Anastasia Shesterinina, distributed under a Creative Commons Attribution ShareAlike 3.0 License. Click image for link."][/caption] Oh, Sir David Attenborough . . . how do I love thee? Let me count the ways. Blue Planet . . . Planet Earth . . . Life in the Undergrowth . . . and a gem I just recently encountered, his 1979 BBC debut, Life on Earth. I haven't seen it, but apparently someone rummaging through a British charity store recently encountered one of only about 100 copies of its score the composer ever pressed, and they're now being offered for sale on CD online. Listening to the meditative and elegant sample tracks of Gymnopedie for Jellyfish, or Arabesque for Flatworms, I am transported back to the nature documentaries that aired on the lazy Sundays of my childhood, in which the pace was slow as molasses and many long moments passed narrator-free so as to better contemplate the mystery of nature. Behold: the brook trout spawning, or the grizzly grabbing salmon. It was a simpler time, when the TV's four channels (CBS, ABC, NBC, and PBS, which in my little remote corner of rural southeast Tennessee went snowy all night, to return to the air early the next morning preceded by the Star Spangled Banner and space shuttle lifting off) were inhabited by the likes of Marty Stouffer's Wild America and Mutual of Omaha's Wild Kingdom(I briefly considered naming this blog wildkingdoms.com, but it turned out the domain was already taken). How I miss them sometimes. I also briefly considered buying the Life on Earth soundtrack, but after doing the Dollar-Pound conversion and learning it'd cost me $21 to buy and ship to Colorado, the cheapnik in me won out. And Life on Earth itself remains out of grasp for now too. Though it has been released to DVD in the UK, the US has not been so fortunate. That is a shame, because the British Film Institute ranked it 32nd in the top 100 British Television Programs of all time, ahead of Walking with Dinosaurs and the 1995 Colin Firth-Jennifer Ehle Pride and Prejudice (Why is that ranked only 99th? Why? Why?) Wikipedia has some sort of conspiracy theory about Life on Earth never being released here because of its (gasp!) explicit evolutionary content, but plenty of other evolution-based programs have been put on DVD here no problem so I have a hard time buying that. Here's a clip (featuring a very young David Attenborough) on the making of it to give you a taste for what you're missing: In any case, we will hopefully soon have the next best thing because we still have D.A. with us, and he has done a bit of a re-do of Life on Earth that is currently airing on BBC One: Life. Though all my British readers may be having a "Duh!" moment here, most of us in America are quite ignorant of it -- or at least I was until about two weeks ago. Let's hope this Life does find a way -- to jump the pond. Have any British readers seen it yet? Any early reviews? And Discovery Channel, if you are reading this, please leave David Attenborough's narration intact in any US broadcasts. No Sigourney Weaver, Morgan Freeman, or (god forbid) Tom Cruise. Your attention to this matter is greatly appreciated. Thank you.

Wiki_Illicium_verum

Jennifer Frazer — Sun, 15 Nov 2009 22:04:44 +0000

wiki_star_anise_fruit

Jennifer Frazer — Sun, 15 Nov 2009 22:08:50 +0000

Star Anise and You

Jennifer Frazer — Sun, 15 Nov 2009 22:17:49 +0000

Plants have been getting short shrift around here lately. It's time to fix that. Sitting in the spice rack of many an Asian home, and a very few American homes, is the unusual looking fruit of an ordinary-looking plant with an unexpected use. Here is that plant: [caption id="attachment_1875" align="alignnone" width="480" caption="Delicious or deadly? Both -- depending on your perspective. Image by Shu Suehiro, licensed under the Creative Commons Attribution 3.0 Unported License. Click for link."][/caption] And here is its fruit: [caption id="attachment_1878" align="alignnone" width="493" caption="Science? Art? My favorite intersection. The shiny objects are the seeds. Image by Bryan Arthur, distributed under the under the Creative Commons Attribution ShareAlike 3.0 License. Click image for link."][/caption] The plant is star anise, Illicium verum. If you know it at all, it is as a spice. As its name implies, its flavor is licorice-y, and indeed the plant makes the same flavoring chemical found in true anise, fennel, and licorice: anethole. It can be used on its own in Asian cooking, but is more commonly known for its inclusion in Chinese five spice powder and Japanese seven spice powder. If you've never tried one of these blends, do yourself a favor take some for a spin.* And now for the use you probably didn't know about: star anise is the raw ingredient used to make oseltamivir, more familiarly known as Tamiflu. The actual raw ingredient is shikimic acid, and many plants, including the North American Sweetgum (with the beautiful genus name Liquidambar) also make it. But star anise is particularly good at making it. The yields are high. It seems odd to think of a modern drug depending on a botanical source, but tamiflu is seemingly still very much in that category. In 2005, shortages in Chinese star anise production caused a shortage of Tamiflu. Nonetheless, it takes some fairly heavy organic chemistry gymnastics to get from shikimic acid to oseltamivir. The wikipedia entry notes, in rather understated language,

Some of the steps in the synthesis require careful handling and relatively mild reaction conditions, as they involve the use of potentially explosive azide chemistry.

Hooo-kay. Having taken organic chemistry, I really do believe that organic chemists earn every penny of their six-figure incomes. You'll also easily realize, if you compare the structures of shikimic acid and oseltamivir, that the Chinese health minister's suggestion that people in China cook their pork with star anise to ward off influenza is absolute rubbish. They look totally different. And if it takes a 10-step process involving “potentially explosive azide chemistry” to get to oseltamivir from shikemic acid, it ain't gonna happen in my stomach. Nor can you get swine flu from pork (duh). Still, pork + star anise could well = tasty. Star anise's price still rises and falls with flu outbreaks, even though 99.6% of last year's seasonal flu was resistant to Tamiflu (a sobering and staggering rise from only 12% the year before) and the same thing could easily happen to pandemic H1N1 flu. Still, so far only 39 of 10,000 pandemic H1N1 flu samples tested positive for resistance to Tamiflu in October. And doctors still turn to Tamiflu to fight this flu. Just a few weeks ago, the U.S. Government decided to release the last of its children's Tamiflu stockpile due to this flu's disproportionate ability to kill the young -- even, disturbingly, some who were apparently otherwise completely healthy prior to infection. But it's hard to believe with hundreds of thousands of doses of Tamiflu flowing into all regions of the U.S. that the drug will last long against the virus. Between this and newly developing E. coli-based shikimic acid production techniques, star anise's run as a flu-fighter will probably be short lived. Next time: The Curious Taxonomy of Star Anise ________________________________________________________________ *Chefs are cooking with five-spice powder more and more as they experiment with traditional ingredients in new cuisines. I often make crispy tofu-ginger fritters with five-spice powder, and I also recently found a recipe in Cooking Light for pumpkin pie with five-spice powder. I bet it'd also be good as a replacement for cinammon in snickerdoodles, since cinnamon is one of the ingredients (in my commercial "Asian Gourmet" blend they are, "cinnamon, anise, fennel, ginger, clove, and licorice root". I note with amusement that makes six.)

wiki_illicium_verum_kohler

Jennifer Frazer — Sun, 15 Nov 2009 23:28:01 +0000

The Curious Taxonomy of Star Anise

Jennifer Frazer — Wed, 18 Nov 2009 14:26:49 +0000

Star anise's job moonlighting as Tamiflu caught my eye because star anise is in a group of plant families with a very interesting pedigree. It is in the Illiciaceae (Ill-ik-ee-ay'-see-ay), a small family whose members are all in one genus – Illicium. There are only about 40 species in the whole family (the pea family, for comparison, contains about 20,000), and their most distinctive characteristic are those beautiful star-shaped fruits, like the brown whorl at left. They are woody trees or shrubs with shiny simple evergreen leaves and special spherical ethereal oil cells (full of anethole, in this case) in the bark, leaves and (obviously) fruit. Like retirees and Mexican drug-lords, they seem to prefer life in the tropics and sub-tropics. The Illicaceae was only the second family of flowering plants I learned in plant taxonomy because it belongs in a very loose group that seem to have split off from the rest of the flowering plants very soon after flowers evolved. Informally called the “basal angiosperms” (angiosperm being the science nerd name for flowering plant -- look for Illicium in the Austrobaileyales on the tree) or paleodicots, scientists agree they parted ways with the rest of the flowering plants early on, but aren't necessarily closely related to each other at all. They're more like a bunch of toddlers who wandered away from the same birthday party: they are connected in at least one basic way, some of them may be closely related, but they can only *sorta* tell us where they came from and who they belong to. What makes the families in this group interesting is that many of them seem to retain the characteristics botanists traditionally considered to be those of the first flowering plants: woody, evergreen, many-petaled, tropcial or semi-tropical. Several, like Illicium, have scattered ethereal oil cells that make them good spices. In addition to star anise, you'll recognize many of McCormick's Greatest Hits here: the family Lauraceae (all plant families end in -aceae) contains Laurus nobilis, Cinnamomum verum, and C. camphora, the sources of bay leaves, cinnamon, and camphor. Piperaceae contains Piper nigrum, the source of black and white pepper. Myristicaceae contains the beautifully-named Myristica fragrans – nutmeg and mace. [caption id="attachment_1923" align="alignnone" width="614" caption="The fruit of Myristica fragrans. The brown nut-like object is the source of nutmeg, while the red alien-goo that looks to be devouring it is the source of the spice mace. True story! Image by Mila Zinkova, licensed under a Creative Commons Attribution ShareAlike 3.0 License. Click image for link."][/caption] But how do we know that woody evergreen plants with flowers with lots of separate parts are similar to the first flowers? Well, we don't for absolute certain, though botanists felt it was true for many years. In fact, recent evidence may be challenging that view. But there are many clues these plants did indeed split from the flowering plants early on. And I'll tell you about them -- and a little about what we know about the first flowering plants -- next time.

Wiki_Nutmeg_Fruit

Jennifer Frazer — Wed, 18 Nov 2009 14:31:41 +0000

Excuse Me Sir . . . My Seal Seems to be Possessed by a Roland Synthesizer . . .

Jennifer Frazer — Thu, 19 Nov 2009 02:31:25 +0000

Taking a break from the heavy taxonomy for a moment, let's have a quick bit of weird wonderfulness. I could not believe my ears when I viewed this excerpt from Werner Herzog's recent film about Antarctica courtesy Zooillogix . . . Wow! Amazing, huh? Though the bit halfway when the researchers listen to the seals under the ice does have somewhat of the feel of the final scene of a local 8th grade production of Hamlet when everyone "dies". In case you don't know Werner Herzog, he is the director who gave us the documentary "Grizzly Man" about Timothy Treadwell. Remember him? He was the man who lived with bears in Alaska and ended by being consumed by one along with his girlfriend while his video camera recorded audio of the whole thing. I quite recommend the film, if for no other reason than to see a portrait of a man consumed by his passion, however misguided, and of the jaw-droppingly gorgeous beauty of the vast remote region of Alaska he lives in. Would that we all could spend a few months there each summer, simply watching the grass get tossed by the wind or the streams ripple over the rocks. Of course, not so much with the getting eaten by grizzlies part. Herzog also famously hauled a 320-ton steamship over an isthmus in Peru for the filming of "Fitzcarraldo" (a feat so Cameron-esque someone else made a documentary about it) and has produced a slew of critically-acclaimed but otherwise little known art house feature films and documentaries. "Grizzly Man" did receive some measure of success and fame, and one of his next films -- "Rescue Dawn" -- was shown widely enough that even my parents saw it. This clip is from "Encounters at the End of the World", which apparently came out in 2007, though I was oblivious. As expected, it has sterling marks on Rotten Tomatoes. It has now been added to the Netflix queue. You can find how seals fit into the mammals here; here's more on Weddell Seals, the composers of this unearthly music.

flickr_alpine_forgetmenots

Jennifer Frazer — Mon, 23 Nov 2009 06:41:57 +0000

flickr_forgetmenots

Jennifer Frazer — Mon, 23 Nov 2009 06:48:44 +0000

flickr_tree_heliotrope

Jennifer Frazer — Mon, 23 Nov 2009 06:53:26 +0000

We're (a Plant) Family?

Jennifer Frazer — Mon, 23 Nov 2009 14:30:00 +0000

This week is Thanksgiving, and with that comes many hours spent cooped up with people you share little to nothing with but genetics. These contrasts typically become most noticeable once some fun-loving soul decides to baste the conversation with unadulterated far-(right/left)wing politics. Isn't family great! : ) Well, the same thing happens in the plant world, though thankfully, since plants can't speak, or truthfully, travel, they don't tend to get in fist-fights over the gravy with their unlikelier kin. The other day I discovered this plant, the tropical tree heliotrope -- also called octopus bush for fairly obvious reasons -- over at Botany Photo of the Day: [caption id="attachment_1963" align="alignnone" width="614" caption="Is it just me or does that plant look like it could use a pair of googly eyes above its flower tentacles? http://www.flickr.com/photos/wlcutler/ / CC BY 2.0"][/caption] Imagine my surprise when I discovered it's in the same family -- the Boraginaceae (bor-aj-i-nase'-ee-ay) -- as the sweet little alpine forget-me-nots I know and love! [caption id="attachment_1960" align="alignnone" width="588" caption="These things smell divine, too. You'd never guess such a little flower could put out such a big, beautiful smell. http://www.flickr.com/photos/99067413@N00/ / CC BY-NC 2.0 Non-commercial use only."][/caption] Such is the power of evolution. Every forget-me-not family member I'd previously encountered had been, well, I believe the PC term is "diminuitive" (being such myself). And then I find this monster. But genes don't lie. If you look very carefully at the tree heliotrope flowers, you will see the resemblance to forget-me-not flowers, and the scorpioid cymes (flower spikes (science-nerd term: inflorescences) with a coiled end like a scorpion's tail) forming the octopus tentacles seem pretty characteristic of the family too (though the presence of 4 little nutlets as fruit is the most diagnostic characteristic of the family). Here's what they look like in a rather more sedate member of the family, another species of forget-me-not: [caption id="attachment_1961" align="alignnone" width="614" caption="Note the scorpion-tail cyme -- it's out of focus but it coils like a backward six that fell over with the ascender pointing left. A second coiled cyme faces us head-on on the left.http://www.flickr.com/photos/dawnzy/ / CC BY 2.0"][/caption] Naturalists (and you and I) can often recognize new members of families like this instinctually using something the Germans call "bauplan", or body plan in English. When you start learning bauplans, you start getting a creepy, deep-in-your-bones feeling you've *seen* some plant or organism before, you just know it, especially if you haven't. It happens with all kinds of creatures, and usually starts to become noticeable after you've spent enough time connecting names with flowers/mushrooms/tentacles and communing with them in the gardens/woods/deep-sea submersible. For example, many times when I'm out in the woods I'll pick up an unfamiliar mushroom and declare -- rather mystically for a person of a scientific bent -- it's got that "Cortinarius" feeling. It's the underlying structural similarities -- the angle of a curling cap, the texture of a petal (the texture of forget-me-not petals is quite distinctive: almost styrofoamy), or in this case, the shape of the flowers and flower-stalks -- between something new and something old that are tipping your brain off and giving you faux deja-vu. It's probably the same feeling you'd get if you encountered one of the many lesser-known Baldwin brothers for the first time. Here is a tree that puts the Forget-Me-Not Family (Boraginaceae) in context -- it's in the asterid mega-clade (would not have guessed a kinship with asters!) and is most closely related to the mint (Lamiaceae), potato/tomato (Solanaceae) and gentian families (Gentianaceae). Back out via the little arrow to the left to put it in larger context. So this week as you're sitting across from your cousin Lloyd, just be grateful that the other 364 days of the year you do not have to listen to the talking points of either Glenn Beck or Michael Moore, and you can bloom happily in your own little garden. p.s. -- Haven't forgotten about finishing up the story of the paleodicots! But they will have to wait until next weekend.

wiki_damselfly

Jennifer Frazer — Sun, 29 Nov 2009 00:45:25 +0000

wiki_dragonfly

Jennifer Frazer — Sun, 29 Nov 2009 00:46:20 +0000

Of Dragons and Damsels Not in Distress

Jennifer Frazer — Sun, 29 Nov 2009 00:54:00 +0000

First, a warning: This clip of a BBC nature documentary is possibly not safe for work. If these were humans . . . Oh. My. Even as is, I'm not sure this would, er, fly on American television. Isn't it cute that they make a heart shape when they mate? It almost makes up for the fact the male has a penis from hell. Although it's by no means the most frightening I've seen. There are many insects (of which bedbugs are a prime example) that mate by "traumatic insemination", in which the male stabs the female with his often-horrible, spiky penis and injects sperm directly into the female's body cavity. [Pause while female readers silently scream in horror.] Brought to you by the James Cameron School of Insect Adaptations Worthy of Sci-Fi Horror Flicks (TM).(Motto: "They mostly come out at night. Mostly.") In any case, notice that these are damselflies. Many people confuse them with dragonflies. Here is your natural history lesson for the day. This is a damselfly: And this is a dragonfly: Note the chief differences: Most damsels neatly fold their wings behind them when they land. Dragons hold them out like biplanes. Careful observers will also note that dragons' wing pairs do not match as closely as damsel wings (the dragonflies' hind wings tend to extend tailward farther) and damselfly eyes are much further separated. Almost googly, one might say. Here's a tree to show you how they're related. Their clades' (groups') technical names are Zygoptera (damselflies) and Anisoptera (dragonflies). Notice that the uneven wings are right in dragonflies' formal name: an-iso-ptera: "not -- same -- winged". They're both in the insect order Odonata; back out via the little arrow on the left to see how they fit into the Insects.

Did I Entertain/Educate You? Nominate Your Blogger for Inclusion in Open Laboratory 2009

Jennifer Frazer — Mon, 30 Nov 2009 04:21:01 +0000

UPDATE: Broken links fixed! UPDATE2: Oops -- It looks like the deadline is actually Tuesday at midnight. You can still submit if you like, but the organizers ask you don't submit anything that's already listed here. Thanks! : ) Hi everyone. Sorry this is a bit last-minute, but I didn't realize the deadline for this was upon us. The Open Laboratory is a dead tree book containing "The Best Writing on Science Blogs", and YOU can nominate posts for it. The deadline for this is Nov. 30 (i.e. Monday) at midnight, which I just learned thanks to a gracious post by Psi Wavefunction. If you particularly enjoyed any of my posts this year, consider nominating one for the book. They do stipulate

Make sure that the submitted posts are possible (and relatively easy) to convert into print. Posts that rely too much on video, audio, color photographs, copyrighted images, or multitudes of links just won't do.

which is unfortunate, because I try to make an effort for every post to include video, audio, color photographs, and multitudes of links. Isn't that what writing for the web is about? Still, please consider nominating anything you particularly enjoyed. It's fast and easy to do right here. Posts that might be suitable include Moss that Swings Both (All?) Ways and its sequel, The Six Million Dollar Moss: Why Biology is WAY Cooler than Nuclear Physics, More Bad News for Bats: Marburg Virus Edition, and When Plesiosaurs Ruled the Sea, but really, knock yourself out if you have a particular favorite.

wiki_Haeckel_Copepoda

Jennifer Frazer — Thu, 03 Dec 2009 01:38:37 +0000

Is Biodiversity More or Less Threatened Than We Thought?

Jennifer Frazer — Thu, 03 Dec 2009 02:37:26 +0000

[caption id="attachment_2035" align="alignleft" width="426" caption="Ready for the Vegas floor show: marine copepods, by the incomparable Haeckel. In Kunstformen der Natur, 1904. Click image for source and species IDs."][/caption] You all have gathered, I'm sure, that I have a love/hate relationship with the term "biodiversity". There's nothing inherently wrong with it, but it gets used so much in so many vague ways that I feel it turns a lot of people off to the subject in the same way "family values" and "social justice" do. It's been politicized and corporatized. Still, we must have a term for the idea, and no other word seems to fit quite as well, and even if it did, it would certainly soon suffer the same fate. To that end, I accept and use the term, and present you now with a biodiversity news roundup. First, there is this press release from the University of Oxford highlighting a study recently published in Science. In it, the authors claim life is much more adaptable to climate change than we are giving it credit for. If that's true, I'm all for it! A second article in Nature (subscription required), however, takes an opposite, but not inherently contradictory approach. It notes we are falling woefully short on goals we've set for ourselves for protecting biodiversity in the last five or so years. Then there is this news: Mark your calendars because the UN has decreed 2010 the International Year of Biodiversity, partly in response, I'm sure, to our lack of progress on our goals. I note with consternation, for instance, that the calendar of events for next year does not yet include any events anywhere in the United States, though Cameroon, Indonesia, and Slovakia have all stepped up to the plate. Further highlighting biodiversity's emerging importance, the Smithsonian Institution has announced its Strategic Plan for the years 2010-2015 and they have decided to make biodiversity one of their top priorities: the report designates four "grand challenges", which are "Unlocking the Mysteries of the Universe", "Valuing World Cultures", "Understanding the American Experience", and, of interest to us, "Understanding and Sustaining a Biodiverse Planet". Scientists know the importance of biodiversity, but I often feel the rubber is failing to hit the road when it comes to convincing people why it is important. Some have tried to emphasize the provision of ecosystem services (clean air, clean water, keeping the climate stable for agriculture; in short, preserving a livable planet). This article (subscription required) profiles a woman who's campaigning to save biodiversity with that business-based approach, but it does gently point out that sometimes the best carbon storage or ecosystem services areas aren't always the ones with the highest biodiversity. What then? Well, that's where my efforts (along with hopefully yours and many others) come in. I want to help communicate to the public why these creatures are inherently cool, and no less worth reverently preserving for their own sake than the contents of the Louvre, the city of Pompeii, the original folios of Shakespeare, or Def Leppard's greatest hits. OK, maybe that last one is just me. But you get my meaning: we should protect biodiversity because it's the right thing to do. I don't understand why we aren't pouring more money into this. I'm all for space exploration, but barring hyperspace bypass construction, Mars, Europa, Enceladus, Pluto, and the Kuiper Belt will all be there in 50 years. So will any life they may or may not harbor. A large proportion (up to a third of ALL species by 2050, by some estimates) of mind-blowingly cool Earth species, many of which I've told you about before, may not. Gone forever. If I think about it too hard, it makes me want to cry. Why are we sinking billions into space exploration, and pocket change into ocean exploration and preserving biodiversity? As much as I like fossils, I like the real things much better.

Weird, Wonderful Benthic Squid

Jennifer Frazer — Sat, 05 Dec 2009 04:45:14 +0000

The sort of things we find when we just start looking . . . I really, really, really, wanted to finish up my posts on paleodicots tonight, but it isn't going to happen as I'm leaving town early tomorrow morning for the weekend and still have to pack. So instead, I wanted to give you a taste of all that's out there still waiting for us to stumble upon. The above beauty was apparently found in 2003. Judging by the scientists' reactions, it'd probably never been seen before. What is that thing on its head? I have no idea. Sexually selected cephalopod plumage? A squid spoiler?An HD antenna? Here's a different, identified species (Magnapinna) captured on camera by an oil company (go to youtube for the details). Dear God. if I happened to be underwater and see this live . . . let's just say it'd have a sphincter factor of 9.0. Note the depth in feet. There is so much cool stuff left to discover right in our own back yard. Two other pieces of good/bad biodiversity news today: Biodiversity loss can increase infectious disease in humans and Elevated carbon dioxide may mitigate losses of biodiversity from nitrogen pollution We'll get back to your regularly scheduled programming next time. Happy weekend!

Wiki_Nemertea_Proboscis_worm

Jennifer Frazer — Wed, 09 Dec 2009 15:14:31 +0000

David Attenborough at the Arkive launch

Jennifer Frazer — Wed, 09 Dec 2009 15:36:33 +0000

David Attenborough at the Arkive launch

Jennifer Frazer — Wed, 09 Dec 2009 15:46:38 +0000

Giant Predatory Marine Nemertine Worms Ate My Homework

Jennifer Frazer — Wed, 09 Dec 2009 15:51:43 +0000

[caption id="attachment_2075" align="alignnone" width="576" caption="If you think this is bad, wait till you see the video. A scavenging nemertine worm, cousin of the famed "screaming eels". That fish on the left looks like it has suddenly realized it's headed for the fish stick factory. Photo by Henry Kaiser, National Science Foundation"][/caption] In case you missed it in the last few weeks, BBC's new "Life" series (narrated by the great D.A.!) released an amazing clip of a starfish and marine nemertine (aka ribbon) worm feeding frenzy in McMurdo Sound, Antarctica. They won't allow video embedding, but go here for the superlarge youtube video in all its glory. Be warned that the seal noshing is a bit . . . graphic. If you imagine the seal made from the same stuff as gummy bears or laffy taffy, that might help a bit. Here is another BBC article describing the video. When will we in the United States get to see "Life" in its full glory? Come on BBC, throw us a frickin' bone. We still haven't got "Creation" yet either, though word is it's coming in January. A brief perusal of the wikipedia article on nemertines reveals some compelling details; these worms have probosci that may have poisonous stylets used to attack and kill their prey. This little detail was a particular gem:

The proboscis is wrapped around the prey, which is normally other invertebrates such as crustaceans and annelids and can be many times larger than the nemertean itself, and the prey is then stabbed repeatedly with the stylet until dead.

Awwwwww. The article also sedately notes the worms are documented to reach 30 meters; some reports have indicated they may reach 50 or 60 meters. Ladies and gentlemen, that's almost 180 feet. A blue whale reaches about 90 feet. It seems these worms used to be thought of as closely related flatworms, like the cross-eyed Planaria of biology lab fame. Now scientists understand these worms are more complex than once thought, and more closely related to the annelid worms (which I've written about here before) and mollusks. Here's a nice tree showing the relationship. And just look at all the weird, wonderful life on that tree! Have you even heard of half of those? Finally, just to recap, I [heart] David Attenborough. [caption id="attachment_2083" align="alignleft" width="457" caption="The man himself! How can I lure him to Colorado? Sadly, we have no birds-of-paradise. We have do have birds-of-ridiculous-mating-displays, though, aka sage grouse. Wildscreen's photograph of David Attenborough at ARKive's launch in Bristol, England © May 2003. Creative Commons Attribution License 2.5, click image for link."][/caption] I just watched the first half of Attenborough in Paradise the other night, and his seeming ability to casually drop Alfred Russel Wallace quotes and ad lib arresting narration is astounding. David, I salute you.

EOL_common_skate

Jennifer Frazer — Sun, 13 Dec 2009 00:17:22 +0000

Bad Taxonomy Kills

Jennifer Frazer — Sun, 13 Dec 2009 00:25:20 +0000

[caption id="attachment_2100" align="alignnone" width="460" caption="The common skate, Dipturus batis. This, obviously, is the not-up side, referred to by zoologists as "ventral" (the opposite of "dorsal"). Botanists would call it "abaxial". Image by Misjel Decleer, published under a Creative Commons Attribution Non-Commercial Share-Alike 3.0 license. Click image for link."][/caption] Just in case you thought taxonomy was a strictly useless pursuit . . . . . . and you can see how skates fit into the rest of the cartilaginous fish (fish with cartilage skeletons like sharks) here.

Wiki_Water_lily_in_Japan

Jennifer Frazer — Tue, 15 Dec 2009 15:11:37 +0000

Wiki_lady_slipper_orchid

Jennifer Frazer — Tue, 15 Dec 2009 15:31:16 +0000

wiki_Nep_northiana_pitcher

Jennifer Frazer — Tue, 15 Dec 2009 15:33:09 +0000

Wiki_Nymphaea_alba_water_lily

Jennifer Frazer — Tue, 15 Dec 2009 15:39:16 +0000

Wiki_Nymphaea_alba_water_lily

Jennifer Frazer — Tue, 15 Dec 2009 15:40:36 +0000

Wiki_Amborella_buds

Jennifer Frazer — Tue, 15 Dec 2009 15:42:17 +0000

On the Origin of Flowers

Jennifer Frazer — Tue, 15 Dec 2009 15:45:50 +0000

[caption id="attachment_2111" align="alignnone" width="614" caption="A water lily. There is an evolutionary secret staring right at you in this picture. Can't see it? Read on to find out what it is, then come back here and click on the photo as many times as you can to see it in extreme-close-up-o-vision."][/caption] A few posts ago, I told you that star anise is interesting because it belongs to a group of plants that split from the rest of the other flowering plants early on, and that for a long time, scientists felt plants like these retained a lot of the features of the first flowers. Scientists think that long ago, petals, carpels (the girl bits), and stamens (the boy bits) evolved from leaves. In other words, the leaves were the raw material upon which evolution acted to create a specialized cluster of sexual structures we now call flowers. By this reasoning, a flower is essentially a bunch of colored, modified leaves that the plant has packed together with its gonads at the end of a stem (a pedicel (ped'-i-sell)) for the purposes of luring insects to move pollen from flower to flower, i.e., reproduction. So yes, when you stick your nose in to inhale the perfume of a delicate flower, you are essentially shoving your sniffing nose – doggy-greeting style -- into the flowers' unmentionables. The 3% of plants that are basal angiosperms (the group in which star anise fits) seem to have a lot of the characteristics we'd expect in first flowers. Their flower parts are usually physically separate and little changed from each other, like magnolias or star anise or the water lily above – as if each one evolved from an individual leaf. This is not true of highly derived (changed a lot) flowers like orchids, or this crazy pitcher plant, Nepenthes northiana, with the digital camo in the back of the pitcher and a convoluted and unified structure. Although not a flower, the pitcher is, believe it or not, a modified leaf. Thus petals are essentially colored leaves, and the stamens of many of these groups, particularly water lilies, are essentially petals/leaves with pollen-making chambers on the ends. Some seem to defy classification as either petal or stamen. Click on the picture at the top of the page and keep clicking on it to magnify it. Look carefully at the stamens at the very edge of the bunch -- they are more like purple petals with pollen making slits half way down them than true stamens. In this photo, notice the transitional stamens toward the outside of the center – they also look like a cross between a petal and a stamen, although in this case, the pollen-making chambers (anthers) are at the tip of the petal rather than halfway down. For a while, some scientists felt the first flowers looked very much like magnolias, hence an early term for the basal angiosperms, magnoliids. But that view is changing. Showy magnolias were probably a very early specialization. Scientists have compared plant DNA the same way they compare flower and plant body parts and have concluded the living flower lineage that split the earliest from the rest of the living flowering plants is the diminutive (and threatened) Amborella, pictured here. Very closely related to Amborella at the base of the tree are the water lily family, Nymphaceae (nymf-a'-see-ay), and the Austrobaileyales, the group that includes star anise (see the tree here). Plants in these groups often possess characteristics of both the two major flowering plant groups that comprise the other 97% of plants, the monocots (grasses, grains, lillies, orchids, etc.) and the eudicots (roses, apples, poppies, maples, etc.), giving scientists more confidence that they inhabit a special place at the base of the flowering plant tree. Now scientists believe the first flower was likely to have been small, green, simple, and inconspicuous – not unlike Amborella. Nova did a special on one Chinese aquatic fossil candidate for “the world's oldest flower” in 2007 (see a great short slide show on it here). Though it's interesting that water lilies, also at the base of the tree (look for Nymphaeales), are also aquatic, the status of the fossil -- Archaefructus, or "ancient fruit" -- as "oldest flower" has been challenged. There have been other "most ancient flowers" (Bevhalstia pebja) in the past and will surely be new contenders in the future. So, four weeks and three posts later, it may finally be becoming clear why star anise is such a surprising plant! In addition to the gorgeous and pungent whorled fruits you can use to flavor stir fry pork or decoupage your 70's hippie bus, it is a member of one of the most ancient flowering plant lineages on Earth and could save you from one of the planet's newest viruses.

The Biodiversity of Other Worlds

Jennifer Frazer — Sat, 19 Dec 2009 16:00:04 +0000

Warning: This post contains mild Avatar spoilers. I want to show you something. Pull the slider bar across to 1:37 in this clip of the Jim Henson masterpiece and my favorite childhood film, “The Dark Crystal,” and watch until about 2:33. Amazing, huh? It's made even more amazing by the fact that all these creatures were real tangible things dreamed up and manufactured by the Jim Henson studio. In the making-of documentary, you can see them assembling them by hand like traditional European craftsmen (many of whose skills they used). This was a movie I watched over and over whenever I could on the gigantic early VCR owned by our neighbors down the road in rural Tennessee when I was 5 or 6. I absolutely loved it, even though the first 5 minutes of the were missing because my neighbors were slow on hitting “record”. Even little Jen(me) was fascinated by the diversity of life – even imagined life. Last night I saw Avatar on opening night in 3D on an IMAX screen in Denver, and I got to live this experience all over again. Avatar is not a movie that is long on brains or wit, even by the standards of other James Cameron films. I wish they'd spent half the time on the script they spent on the visuals. You could also compile a list 20 or 25 items long of elements this movie shares with other Cameron films, from big things like a strong female lead (all films), to a soulless corporation driving evil in the name of profits (Aliens, The Abyss, Titanic; which, by the way, is a major reason yours truly has all her money in “socially responsible” investments) down to really subtle details like a supporting female character who's really good at operating an unusual vehicle (One Night in the Abyss) or a bad guy fighting the good guy toward the end of the movie in an unbreathable environment in a machine that gets its front window cracked, thus admitting some of the deadly medium (Michael Biehn's character in the Abyss). But James Cameron films have their virtues, and they are a passionate attention to detail, a high sense of adventure, protagonists you want to love, and really deadly/exotic/fantastically beautiful aliens. In this film, he's taken this latter theme, one he started with the fantastic ctenophore-inspired aliens from “The Abyss” (still my favorite Cameron film) and used it to imagine the biodiversity of another world. For those of us fascinated by life, there is a lot to see and wonder at in this film. It provides, as Manohla Dargis of the New York Times says in her review, the big WOW. Because it's such a magical experience, I'm not going to give much of it away, except to say it's obvious these creatures were inspired at least in part by computer geeks, given that they all have USB ports. But Cameron takes the modus operandi of people trying to re-imagine life on other worlds – putting sea creatures on land or making plants animals, ones which Henson and legendary conceptual artist Brian Froud drew on heavily to imagine the world of the Dark Crystal – and takes it up a notch. In one of my first posts I told you the parasite Giardia resembles the love child of a squid and a kernel of corn. In Avatar, you get to find out what happens when a jellyfish and a dandelion make sweet, sweet love. As has been pointed out by many reviewers, Cameron's narrative breaks no new ground and simply retells some of America's classic, and not always proud stories (Pocahontas, Dances With Wolves) with lesser dialogue and characters. Even the facial structure and ears of the blue alien Na'vi strongly recall those of gelflings, above. But oh, what a world in which to retell our stories. For people who are not biodiversity-philes, this movie takes a bit of the wonder that I easily feel crawling around the Colorado forest floor after a good rain or watching D.A. ramble on in his adorable, thick British accent about marine worms and dumps it right in their laps. Cameron was so attentive to detail there are things in "Avatar" for even lichenologists and bryophiles to love. I won't give it away, but when you first see the rainforest of the forest moon Pandora (wait a minute . . . Endor? Pandora? ) through the avatars' eyes there is a tiny 3D detail that will take your breath away. Though sadly, this biodiversity afficianado has never been to a real rainforest (it's up there on my list of dreams along with traveling to the deep sea in a submersible), Avatar puts me as close as I'm likely to get for a while, and it does so in glorious 3D. I've never heard so many audible “wows” from an audience, myself included. Thank you, Mr. Cameron.

Wiki_Leeuwenhoek_xylem

Jennifer Frazer — Wed, 23 Dec 2009 06:52:35 +0000

The van Leeuwenhoek is in the Gallery Just Down the Hall . . .

Jennifer Frazer — Wed, 23 Dec 2009 23:06:21 +0000

[caption id="attachment_2170" align="alignleft" width="404" caption="An Antony van Leeuwenhoek original: Portrait of the Ash Tree as a Young Cross Section. "][/caption] When it has a Water Flea Circus, a Rotifer Room, and a Radiolaria Lounge you know this blogger is going to love it, and the Micropolitan Museum of Microscopic Art Forms is home to all these things. The website, proudly presented by the Institute for the Promotion of the Less Than One Millimetre, is the labor of love of Dutch artist Wim van Egmond. If you just want the highlights, here's a nice slide show by Wired Magazine. Following in the steps (or perhaps slides) of his famous countryman and father of microbiology Antony van Leeuwenhoek, Wim has not only produced a great collection of microscopic photos, he's got a great collection of microscopic photos in 3D, a technology sadly not available to the great microscopist. And as we know from our Avatar experience, everything's better in 3D . . . . You'll need a cheap pair of red-blue glasses in order to experience the 3D. I highly recommend investing or procuring such, since there's a lot of great 3D space images also getting tossed around the internet lately. Antony (Antonie) van Leeuwenhoek (Lee-oo-ven-hoke Lay'-oon-hook -- I think. Please correct me if I'm wrong, Jasper) is a guy you should know about if you read this blog. He was a Dutch cloth merchant who took up microscopy in the mid-1600s; met Peter the Great and may have known Johannes Vermeer (my favorite painter); and may have been the first human ever to see and draw microorganisms, which he called (delightfully) "animalcules". He lived to be 90 -- no small feat in the 17th century, and a reminder of how rugged humans can be even in the absence of antibiotics, toothpaste, text messages, etc., etc. He mastered a technique for making a small and optically excellent microscope that is essentially a melted bead of glass. It is so simple you can teach schoolchildren to make them in a few minutes, as protistologist Patrick Keeling has figured out how to do. Yet van Leeuwenhoek wanted to maintain his microbial monopoly so he could get the glory for his accomplishment (understandable but rather stifling to science, it must be said). So he seems to have let on like he spent hours in the kitchen grinding lenses to get his beautiful pictures. Hours. [Wipes dewy brow while letting out long-suffering sigh] Above you see one of Van Leeuwenhoek's actual drawings. It's remarkably accurate (he certainly spent hours on that) and shows the cross section of a one-year old ash tree. The big holes are the vessel elements and the small holes are tracheids, the two chief cell types of wood (which is mostly xylem (zy'-lem)) in flowering plants. These cells move water and minerals when they are new, and once defunct, provide structural support. Thus, when you hold a piece of wood, you're the holding the lignin and cellulose skeletons of tracheids and vessels. You can see that early in the year, the tree made lots of big vessels for pumping water into swelling leaves, while later in the year the flow slowed. This annual variation in vessel/tracheid size is responsible for the growth rings you see in angiosperm (flowering) trees. Those big vessels are a flowering plant innovation that conifers lack, and may be partly responsible for their evolutionary success. It should also be said that vessel elements and tracheids are among the most beautiful (and abundant) tissue-class cells on the planet, thanks to their lignin-thickened decorations. See some more here and here and I believe in Fig. 1(?) in van Leeuwenhoek's drawing above. Way cool! Must get on top of getting a microscope. Must. Must.

fleming_three_slime_molds

Jennifer Frazer — Thu, 24 Dec 2009 16:27:30 +0000

Give the Gift of Slime

Jennifer Frazer — Thu, 24 Dec 2009 16:47:56 +0000

[caption id="attachment_2194" align="alignnone" width="616" caption="Earth: Where Wonders Never Cease. A study of three slime molds by the amazing Kim Fleming, photographer of this blog's masthead. Used with permission. http://www.flickr.com/photos/myriorama/ / CC BY-NC-SA 2.0"][/caption] If you're a reader of this blog, you're probably like me: you love life on Earth. If you're still struggling for a gift for someone and know they feel the same, consider a donation in their name to a conservation organization. The Nature Conservancy or the relatively new charity Oceana are two large conservation organizations with high Charity Navigator ratings. We all know these sorts of places market themselves with photos of polar bears and whales, but the fact is that preserving land and sea for these charismatic megafauna (and this is the reason they use this term -- because the public likes and tends to relate to them) also protects our charismatic microfauna -- slime molds, sea cucumbers, ciliates, etc. -- and the organizers of these charities know this and use them thusly. That's fine with me if people need cute and cuddly in order to justify saving something, but as you know, the raison d'etre of this blog is to show you why the weird and wonderful provide every bit as much reason, if not more. If you don't have any more gifts to buy, consider making a gift of your own this holiday season to one of these two charities or the conservation organization of your choice -- there are many. There are other low-cost, free, or money-saving ways you can help the crazy creatures of the planet in the coming year, too, and I here suggest only a few: conserve the resources you use; lower your carbon footprint; volunteer for a citizen science project (like a backyard bird count or bioblitz); eat less meat (chopping down the rainforest to grow soybeans for animal feed is a major cause of rainforest loss, and my slime mold buddies love to hang out in rainforest. Cows make lots of greenhouse gases too); use a Seafood Watch wallet card to make good choices when you do buy seafood in restaurants or markets; have fewer children (notice I'm not saying have *no* children, although that's perfectly fine for those so-inclined. However, I do believe humans are very much part of the weird wonderfulness of the planet and that having a few children (and teaching them about life!) is a good thing for those so-inclined); buy less new stuff; take a child (or a friend!) to an aquarium or zoo; and talk to other people about amazing, celebrity-shy creatures of the planet in a non-obnoxious, engaging way. In my opinion, the carrot is a much more effective way to influence behavior than the guilt-trip-based stick. I'm going out of town in a few days and will be out of web contact for about a week or so. I wish you all a joyous holiday season!

The Sublime Dance of the Weedy Sea Dragon

Jennifer Frazer — Sat, 26 Dec 2009 17:19:11 +0000

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

Wiki_Rinderpest

Jennifer Frazer — Mon, 04 Jan 2010 14:24:42 +0000

Countdown_savebiodiversity150

Jennifer Frazer — Thu, 07 Jan 2010 06:20:13 +0000

Does Hallmark Make a Card For International Biodiversity Years?

Jennifer Frazer — Thu, 07 Jan 2010 06:51:28 +0000

. . . 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! 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.

Wiki_red_alga

Jennifer Frazer — Sun, 10 Jan 2010 22:44:31 +0000

The Sexual Disability of Red Algae

Jennifer Frazer — Sun, 10 Jan 2010 22:59:35 +0000

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! [caption id="attachment_2250" align="alignnone" width="598" caption="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."][/caption] 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!

Wiki_copepod

Jennifer Frazer — Tue, 12 Jan 2010 04:15:26 +0000

Extinction by Design: Rinderpest

Jennifer Frazer — Wed, 13 Jan 2010 15:43:26 +0000

[caption id="attachment_2223" align="alignnone" width="583" caption="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."][/caption] 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.

Extinction by Design: Guinea Worm

Jennifer Frazer — Mon, 18 Jan 2010 18:18:41 +0000

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? [caption id="attachment_2262" align="alignnone" width="597" caption="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."][/caption] 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.

Wiki_nematodes

Jennifer Frazer — Mon, 18 Jan 2010 18:27:46 +0000

Wiki_Dracunculus_medinensis

Jennifer Frazer — Mon, 18 Jan 2010 18:30:17 +0000

wiki_Treponema_pallidum

Jennifer Frazer — Sat, 23 Jan 2010 05:06:54 +0000

Gorgeous Corkscrews from Hell

Jennifer Frazer — Sat, 23 Jan 2010 05:23:50 +0000

So I haven't managed to get around to writing the post I had bee. . . look! Shiny! Spirochetes! [caption id="attachment_2316" align="alignnone" width="531" caption=""Treats? Where!?" The social bacterium Treponema pallidum. (Subtle, very subtle)"][/caption] 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 . . .

wiki_Blueberry_flowers

Jennifer Frazer — Wed, 27 Jan 2010 03:10:11 +0000

wiki_Corpse_plant

Jennifer Frazer — Wed, 27 Jan 2010 03:23:14 +0000

wiki_Red_indian_pipes

Jennifer Frazer — Wed, 27 Jan 2010 04:06:25 +0000

Your Daily Parasite Fix: The Corpse Flower

Jennifer Frazer — Wed, 27 Jan 2010 04:25:40 +0000

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. [caption id="attachment_2339" align="alignnone" width="597" caption="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."][/caption] 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. [caption id="attachment_2336" align="alignnone" width="593" caption="Vaccinum (blueberry) flowers. Photo by Thomas Kriese. Creative Commons Attribution 2.0 Generic License. Click image for link."][/caption] 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. [caption id="attachment_2347" align="alignnone" width="596" caption="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."][/caption] 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.

flickr_physarum_polycephalum

Jennifer Frazer — Mon, 01 Feb 2010 04:32:50 +0000

The One Cell Planning Commission

Jennifer Frazer — Mon, 01 Feb 2010 05:23:46 +0000

[caption id="attachment_2368" align="alignnone" width="575" caption="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."][/caption] 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".

Oceans: A New Film by the Greatest Nature Documentarian of All Time (IMHO)

Jennifer Frazer — Wed, 03 Feb 2010 04:51:54 +0000

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 "Microcosmos" apart 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."
Read more: http://www.time.com/time/arts/article/0,8599,1957939,00.html#ixzz0eLpwgXH8

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. ------------------------------------------------------------------------------------------------------------------ * 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. : )

wiki_anchiornis_huxleyi

Jennifer Frazer — Sat, 06 Feb 2010 14:48:37 +0000

Dinosaur Color: No Longer a Wing and a Prayer

Jennifer Frazer — Sat, 06 Feb 2010 15:36:05 +0000

[caption id="attachment_2427" align="alignnone" width="576" caption="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."][/caption] 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.

Upupa, Oprah. Oprah, Upupa.

Jennifer Frazer — Tue, 09 Feb 2010 03:22:27 +0000

Good news, everyone! No, really! The approximate U.S. release date for BBC's new nature-glam documentary "Life" has been set. It will be sometime this March on the Discovery Channel, according to wikipedia, but sadly, BBC has willfully ignored my helpful suggestion *not* to replace David Attenborough's narration with a pedestrian American track by Sigourney Weaver, Morgan Freeman, Tom Cruise (the horror!) or the like. Instead, they have chosen . . . . Oprah. Sigh. This is a woman who, though I greatly respect her talent and success, has showcased some pretty anti-scientific views. BBC! Next time . . . [Makes phone sign while mouthing words "call me"] Anytime. Any place. This melodious American voice is all yours -- and I even have voice-over experience. Here's a further taste of the delights that await us (with the correct Attenborough narration): Life - Venus Flytraps: Jaws of Death - BBC One from Paulo Martins on Vimeo. Is it just me or do those hairs remind you of the time-delayed booby traps laid for Indiana-Jones style adventurers in gold-laden caves? You know, the kind where you rest your arm on a stone projecting from the wall, and 10 seconds later it starts moving into the wall as the ceiling sprouts spikes and assumes skewering speed? Yeah. I really did feel bad for the little flies after they got trapped, though. Although their slurping of nectar with that repulsive labellum-tipped proboscis really was revolting (where has that been?) and I have no qualms about mercilessly swatting them around my home, they are living creatures too, and their little cries of despair were truly pitiful. Perhaps I'd make a good Jain after all. Venus flytraps are in the Droseraceae, the Sundew Family, along with the sundews and a curious little package called the waterwheel plant, which is essentially an aquatic flytrap, but sadly does not occur in the western hemisphere. This family is in the Caryophyllales, a group of related plants that have evolved many ways of living in nutrient-poor and/or hot, dry soils. These include clever heat-beating photosynthetic adaptations (C4 and CAM for you biogeeks in the know), salt-secreting glands, and insect carnivory. See here for an idea of their place on the tree of life (click on the arrow to the left to back out and get a bigger picture). In case you're wondering, the title of this post is both a reference to the infamous "Uma, Oprah" David Letterman debacle at the 1995 Oscars and to the bird Upupa epops, the hoopoe (pronounced hupu), which happens to have the favorite scientific name of my friend and birdsong enthusiast Nathan Pieplow, who blogs over at earbirding.com.

Site News: Underwater Blogger, Dividing Amoebae, and a Biology Blog's Host (Server)

Jennifer Frazer — Fri, 12 Feb 2010 17:30:28 +0000

Can there be too many jellyfish at one biology blog? No. No, there can't. This is the famous Jellyfish Lake on the island of Palau, where jellyfish cut off from the sea 12,000 years ago have evolved into docile migratory creatures that live off the food produced by their symbiotic algae. That shot downward into the depths is my favorite. I post it here to celebrate the fact your blogger has decided to take the plunge and become a certified diver. Though I live in landlocked Colorado, life is too short not to experience ocean life the way I experience land life -- particularly for a person with a passion for biodiversity. If I'm ever going to achieve my dream of swimming with whales, it's a fairly necessary step. Plus I found out about an incredible dive in Hawaii where they take you out at night in 7,000 feet of water, drop you down on a tether 40 feet, and let you watch the nightly ascent of the crazy-cool pelagic (deep ocean) bioluminescent organisms -- jellies, ctenophores, crustaceans, etc. Something about the thought of floating out in the Pacific Ocean in the dark with 7,000 feet of water below and glowing organisms all around sends shivers up my spine. It's the best possible sort of ocean documentary -- the one you're starring in. As soon as I discovered it, I knew I must do it before I die, and the only way to get there is to get SCUBA certified. Q.E.D. (although we'll see if I'm still singing that tune when I get my credit card bill this month. : ) ) In other news, I have just re-upped on the web address for this site and purchased a few more for good measure. Hence theartfulmaoeba.com has now divided into artfulamoeba.com, theartfulamoeba.net, theartfulamoeba.org, and theartfulamoeba.info. You can reach me by any one you choose. Knock yourself out. At some point I will also move this blog to my own host service. You may have noticed it is currently hosted at frazer.northerncoloradogrotto.com. That is because the webmasters at my caving club and kindly agreed to lend me some of their unused space. But it would be nice for the domain names for this site to be consistent, so one day soon I'll move it over and all the frazer.northerncolorado.com links will break. I want to tell you now (and will remind you frequently) so anyone who has linked here has plenty of warning. If you are linking to the blog as a whole, theartfulamoeba.com will always work. Happy Friday! Jen

CDC_vibrio_cholerae

Jennifer Frazer — Sun, 14 Feb 2010 20:30:48 +0000

Wiki_Cholera_Death

Jennifer Frazer — Sun, 14 Feb 2010 20:40:46 +0000

Wiki_Cholera_bacteria_SEM

Jennifer Frazer — Sun, 14 Feb 2010 23:04:47 +0000

The Seafaring Killer Bacterium

Jennifer Frazer — Sun, 14 Feb 2010 23:19:01 +0000

[caption id="attachment_2475" align="alignnone" width="603" caption="Still Life with Vienna Sausages with Tails: A Choleric Work in the Style of Pollack. Photo courtesy CDC Public Health Image Library, Image #1034."][/caption] Vibrio cholerae is a bacterium of surprising adaptability, tenacity, and Olympic-class swimming ability. Cholera bacteria can swim in both freshwater and saltwater (a feat most fish cannot manage), and somehow also manage to do the backstroke through stomach acid without kicking the bucket. The historic killer has just popped up again in Papua New Guinea for the first time in 50 years, killing 40. Officials are worried that it may once again become endemic there, taking up residence in the locals' water supply. And this is despite our knowing exactly how to prevent the disease for well over 150 years, ever since British physician John Snow famously helped halt a London cholera epidemic by persuading the authorities to abscond with the handle to the Broad Street Pump, preventing people from drawing its lethal waters. There's only so much science can do. Money and competency are also required.

King Cholera

Cholera is a disease you have probably at least read about if you did any of the required 19th-century high-school lit reading. That's because it was a newly famous and successful killer that century, decimating millions globally and hundreds of thousands in the United States, as the bacteria spread along coasts and up and down rivers. It was a swift death, too, and until mid-century, no one knew the cause. A few years ago I visited some old graves out on the lonely prairie of Nebraska near the inland-sea-sized Lake McConaughy at Ash Hollow State Park. Buried there was Rachel Warren Pattison, a young woman who traveled the Oregon Trail in perfect health one day and was dead of cholera the next. Her party, including her 23-year-old husband of two months, Nathan, had only a few hours to carve a marker for her before the wagons moved on, and miraculously, in an uneven but serviceable hand on a rough stone, they did. I stared at that marker a long time. Sometimes I think modern, first-world citizens greatly take for granted the fact that most of us will not randomly keel over tomorrow from some fatal and unpreventable disease. Before the 20th century, people everywhere lived with that fear (and reality). Imagine how your life would be different if you lived with that reality now. [caption id="attachment_2480" align="alignleft" width="278" caption="Cholera, Bringer of Death"][/caption] In any case, Rachel was but one of the 6,000-12,000 killed along the Oregon, California, and Mormon Trails between 1849, the year of the gold rush, when cholera was spread along the trail by prospectors and settlers, and 1855, when the pandemic ended. And that epidemic was just one tiny sliver of the half dozen major pandemics that covered the world that century, a product of globalization and colonialism. Before 1816, cholera seems to have been a local disease restricted to India. But with people increasingly traveling between east and west, it swiftly leached into waterways around the globe. In the UK, where the disease claimed tens of thousands of lives in the first wave in 1831-32 alone, it began to be called "King Cholera". What made and still makes cholera such a frightening disease was the speed with which it could (and can) kill. Death can come as quickly as 3 hours after the onset of symptoms, but more commonly within 24 hours. Its most famous symptom -- thin diarrhea descriptively called "rice-water" stool -- accurately indicates the cause of death. You die from lack of fluids. That's it. Cholera bacteria use their tails (flagella) to propel themselves into the walls of your intestinal cells, where they secrete a toxin that causes cells to expel chloride ions. This, in turn, creates ionic pressure that keeps sodium from entering cells. That causes osmotic pressure to build on the outside of the cell, drawing massive amounts of fluid into the intestine. Building reliable sewage and water treatment plants prevents deaths, as does simply keeping cholera victims hydrated with a simple electrolyte solution. That we can't manage even that that in many parts of the world is as discouraging as it is laughable.

Ancestors in the Deep

But here's the really interesting thing about cholera, at least from my perspective: scientists are discovering that cholera seems to be an inherently aquatic and previously deep-sea bacterium that evolved to peacefully colonize copepod shells and mollusc interiors, and only accidentally turned out to be good at violently colonizing human small intestines. Wow! In 1999, the submersibles Alvin and Nautile visited hydrothermal vents at the East Pacific Rise and sampled sulfide chimneys there. Vibrio species were identified there with "significant similarity" to V. cholerae, according to past NSF-director Rita Colwell, who has studied cholera since the beginning of her career. Modern V. cholerae colonize the outside of copepod shells (Remember copepods from here and here?) and the insides of shellfish and must compete for space there in the life-sustaining biofilm. It turns out that those that are best at attaching to copoped shells also happen to be most pathogenic in humans. And a mucinase (enzyme that breaks down intestinal mucus) that helps them attach your intestines is greatly aided in its work by the addition of an extract made from mussels. That is, eating shellfish contaminated with cholera make make matters way worse than simply drinking the bacteria. [caption id="attachment_2486" align="alignnone" width="618" caption="Deadly cheetohs: cholera bacteria en masse. One micrometer scale bar is below at left. Courtesy Dartmouth Electron Microscope Facility."][/caption]

Living with Vibrio

Cholera is probably not an eradicable disease, according to Colwell, since we seem to be only accidental victims, while copepods and cholera are the real story. Since they're ubiquitious and may be providing some important ecological function, we must instead rely on ingenuity and engineering to keep us safe. Basic sewage and clean water systems for all people of Earth does not seem like an unreasonable demand. Two interesting human genetic notes regarding cholera: you may already know that Sickle Cell Anemia is widely considered to be a by-product of the genetic advantage that having one copy of the harmful gene provides during malaria infection. With one copy, you get malaria protection; with two copies, you get sickle cell anemia. Some have speculated that cystic fibrosis is a two-copy gene problem produced by a single copy that confers resistance to cholera. As well, blood types seem to confer various protections (though not immunities) from cholera: AB blood is most resistant, followed by A, then B, then O. Vibrio is in the gamma-proteobacteria, a group you can find on the tree of life here (click on Proteobacteria to drill it down a bit). Gamma-proteobacteria contain many human pathogens, including Yersinia pestis (the cause of plague), Salmonella, Escherichia coli, and Pseudomonas aeruginosa, a cause of lung infections in (ironically) cystic fibrosis patients and other ill people. But don't get the idea that gamma-proteobacteria are mostly human pathogens. My gut(!) tells me they're probably the exception, rather than the rule. We just happen to know more about them because there's money to study human pathogens. The rest of the (probably amazingly interesting) group languish in obscurity. Don't believe me? Look at all the families here.

mycologia_psathyrella_underwater

Jennifer Frazer — Fri, 19 Feb 2010 06:07:24 +0000

mycologia_psathyrella_underwater

Jennifer Frazer — Fri, 19 Feb 2010 06:16:52 +0000

The Mushroom that Sleeps with the Fishes

Jennifer Frazer — Fri, 19 Feb 2010 16:56:00 +0000

NOTE: Correction below. Well, this brings new meaning to the concept of gilled mushrooms. Scientists have stumbled upon the first mushroom that fruits underwater, as proudly displayed on the cover of this month's Mycologia. Notice the little bubbles on the outside of the mushroom. On aquatic plants (like the moss to the left), bubbles form because the plant is producing oxygen via photosynthesis. On the mushroom, the bubbles are probably the product of respiration, which means they are filled with CO2, not O2, as the mushroom "breathes".Yes, fungi burn sugar with oxygen to produce energy and CO2 just like we do, but you can see it here because the fungus is underwater*. Way cool! (CORRECTION: HeyPK points out in the comments that CO2 is highly soluble in water (true -- at 20C in freshwater, the solubility limits are 1.45 g/L for CO2 vs. 9 mg/L for O2) so the bubbles are more likely more oxygen bubbling out of the supersaturated stream using the mushroom as a substrate much the way the CO2 in carbonated beverages comes out of solution on ice in glasses. Oops! Sorry for the mistake readers -- I'm still learning too. I'm sure I'll make more from time to time despite my best efforts so please do help me fix them when you see them and I will post a prompt correction. : ) ) According to the good folk over at MycoRant, where I discovered this, scientists had never looked for mushrooms underwater before, but that didn't mean they weren't there. Brit Bunyard, editor of Fungi, speculates there may be a whole world of aquatic mushrooms out there we didn't know about because we never really looked. If so, he noted at MycoRant, it would not be the first time that happened. The mycologist Cecil Terence Ingold (who as of last year was still alive at the age of 104) stumbled upon an entire world of virtually undescribed fungi living in ephemeral forest pools and trickling streams:

In 1937 Ingold moved to University College, Leicester, where he “became excited by the chytrids attacking planktonic algae”. It was his discovery of one particularly beautiful such chytrid (Endocoenobium eudorinae) that reportedly caused him to specialize thereafter in mycology rather than plant physiology; and the next year, while searching for chytrids in a small brook near his home, he found in the stream scum an “abundance [of] many kinds of most extraordinary fungal spores”, most of which were large and tetraradiate in shape. For several months he continued to find such spores in scum, and he finally discovered their source to be fungi living on submerged alder leaves in the stream bed. He later learned that a few such fungi had been described earlier, but, he thought, “rather inadequately”; and so he undertook to classify those aquatic hyphomycetes into eight new genera, all of which remain valid today.

They are sometimes called the "Ingoldian Fungi" in his honor. The incredibly beautiful spores of these fungi (often called amphibious or aero-aquatic fungi or aquatic hyphomycetes), in addition to being star-shaped, whorled, knobbed, or otherwise tricked out in the most wonderful fashion, are hollow when found in still pools -- so they can float and get first crack at the ecosystem's power source: leaves that have just dropped to the water's surface. Dear readers, there's a whole crazy world of living things out there, often invisible to the naked eye but fabulous beyond belief, even in an otherwise unexciting-looking puddle in the forest outside your door. All we have to do is look. _____________________________________________________________________ *And by the way, the gills in mushrooms are for maximizing the spore-making surface area, not for maximizing the gas-exchange surface. Most mushrooms are small enough the CO2 just diffuses out passively (giant puffballs notwithstanding).

NOAA_dinoflagellate_plankton

Jennifer Frazer — Mon, 22 Feb 2010 02:49:56 +0000

Extreme (Plankton) Closeup!

Jennifer Frazer — Tue, 23 Feb 2010 05:21:45 +0000

[caption id="attachment_2547" align="alignnone" width="606" caption="Punk rockers are clearly dinoflagellate posers. Is it just me or does (a) appear to be a member of the House Harkonnen? Dinoflagellate micro-plankton of Atlantic tropical waters. P. 75. In: "Aus den Tiefen des Weltmeeres" by Carl Chun, 1903. NOAA Photo Library."][/caption] Most people have only seen plankton in crappy, fuzzy photos in college textbooks, if they've seen it at all. If you have heard of it, it's probably in the context of the stuff baleen whales eat, and that's about it. I personally was lucky enough to see an entire jar of the delicacy when I visited the Smithsonian's Sant Ocean Hall last fall. It looked a lot like the larvae of the neural parasites that took over the brains of the Federation's top brass in the first season of Star Trek: TNG. Mmmm, mmmm good! Plankton is not a taxonomic/phylogenetic group like most of the things I write about on this blog. Plankton instead refers to any sea creatures that drift. That can include things as large as jellyfish, but typically plankton are much smaller and include things as small as the bacteria, archaea, and viruses with which the oceans teem. The phytoplankton, or photosynthesizing component, are responsible for half of the oxygen you breathe. Well, someone's finally taken some skillful, beautiful pictures of the plankton and they've gone on display at the London Zoo in honor of the Royal Society's 350th Anniversary (Dang! That Society's been around over 100 years longer than my country!). Over at the BBC there is a don't-miss slide show of the exhibit, narrated by the scientist photographer, Dr. Richard Kirby. Let me repeat that: DON'T MISS THIS SLIDE SHOW. You'll get to see how evolution has taken body plans on some interesting trips, as larvae that retain ancestral forms metamorphose into sea creatures you are more likely to recognize. The squid-like larval origin of starfish, in particular, is a fascinating thing. One final note -- Dr. Kirby mentions that plankton are responsible for the characteristic smell of the sea. That is not surprising to me. When I was a grad student in plant pathology at Cornell, I was startled one day to discover that dirt doesn't smell like dirt. Dirt smells like the bacteria that are living in dirt. In one lab we were allowed to sniff (I believe "waft" is the preferred term) a pure culture of soil bacteria. It was a clear agar dish with opaque colonies of bacteria. But it smelled just like fresh topsoil or a cave -- dirty, earthy, wonderful. Discovered thanks to the fine staff of Deep Sea News.

Wiki_Tolkien_1916

Jennifer Frazer — Thu, 25 Feb 2010 15:04:59 +0000

flickr_larches_dolomites

Jennifer Frazer — Thu, 25 Feb 2010 15:07:04 +0000

wiki_larch_cones_needles

Jennifer Frazer — Thu, 25 Feb 2010 15:11:28 +0000

Tolkien the Botanist and the Tale of the Larch

Jennifer Frazer — Thu, 25 Feb 2010 23:04:33 +0000

[caption id="attachment_2572" align="alignleft" width="327" caption="Tolkien during World War I"][/caption] I am rereading The Lord of the Rings, as I do every four years. You only get to read it so many times before you die, and I have determined four years is the ideal interval for me. As always, I am struck by what a fine botanist Tolkien was for a man with a Ph.D. in linguistics.

South and west [Ithilien] looked towards the warm lower vales of Anduin, shielded from the east by the Ephel Duath and yet not under the mountain-shadow, protected from the north by the Emyn Muil, open to the southern airs and the moist winds from the Sea far away. Many great trees grew there, planted long ago, falling into untended age amid a riot of careless descendants; and groves and thickets there were of tamarisk* and pungent terebinth, of olive and of bay; and there were junipers and myrtles; and thymes that grew in bushes, or with their woody creeping stems mantled in deep tapestries the hidden stones; sages of many kinds putting forth blue flowers, or red, or pale green; and marjorams and new-sprouting parsleys, and many herbs of forms and scents beyond the garden-lore of Sam. The grots and rocky walls were already starred with saxifrages and stonecrops. Primeroles and anemones were awake in the filbert-brakes; and asphodel and many lily-flowers nodded their half-opened heads in the grass: deep green grass beside the pools, where falling streams halted in cool hollows on their journey down to Anduin.

Wow. Say it aloud: "deep green grass beside the pools, where falling streams halted in cool hollows on their journey down to Anduin." Tolkien spent lots of time exploring bog and field in his childhood, and his mother Mabel taught him botany,

and awakened in him the enjoyment of the look and feel of plants.

I, too, spent many long hours as a three-, four- and five-year-old exploring the hills, fields, and streams around my birthplace in southeast Tennessee, where wild blueberries grew next to waterfall-fed pools and the iron-oxide dirt stained my socks pink to the eternal chagrin of my mother. Take-home lesson: If you have children, don't be a paranoid helicopter parent. To the extent possible, live near natural areas, and let your children build their imagination and love of nature by exploring them on their own. In any case, I want to take a closer look at one plant Tolkien mentions. Here's another excerpt from the text just before the last passage:

The long journey from Rivendell had brought them far south of their own land, but not until now in this more sheltered region had the hobbits felt the change of clime. Here Spring was already busy about them: fronds pierced moss and mould, larches were green-fingered, small flowers were opening in the turf, birds were singing. Ithilien, the garden of Gondor now desolate kept still a dishevelled dryad loveliness.

Observe: "larches were green-fingered." You may be tempted to think larches are some sort of broadleaf shrub or tree. You'd be wrong. Larches (genus Larix) are a very unusual thing: a deciduous conifer. That's right -- though they are firmly ensconced in the ancient and aristocratic Pine Family, their needles turn gold or brown and drop every autumn, and new green needles take their place every spring. [caption id="attachment_2573" align="alignnone" width="619" caption="Browning larch trees in autumn near the Dolomites in Italy. http://www.flickr.com/photos/krossbow/ / CC BY 2.0"][/caption] Another interesting thing about larches is their needles grow in whorls. Observe: [caption id="attachment_2576" align="alignnone" width="615" caption="Male cones of the larch near needle-whorls."][/caption] For those of you who may be wondering how to recognize this tree from quite a long way away, here's a helpful instructional film: Alas. None of the American larches -- Tamarack, Western, or Subalpine -- grow in Colorado, so I will not be recognizing them from near or far anytime soon. _____________________________________________________________ *A plant's "goodness" or "badness" depends on the context. Tamarisk, which Tolkien mentions in the first passage in a scene intended to evoke beauty and goodness, is also called salt cedar in the United States, and is an imported cone-bearing shrub that has caused endless migraines for land managers across the west. Planted for erosion control by the millions during the Great Depression, it has proceeded to invade the banks of most waterways, siphoning billions of gallons of precious western water out through the tiny openings, or stomata, of its leaves to be wasted in the air and crowding native plants like willows and cottonwoods out of their habitats. In Eurasia, it's a natural part of the landscape. Salt cedar, by the way, is not actually a cedar but a flowering plant. It just looks like a cedar. Pesky common names!

A Moment of Zen: The Clark's Grebes' Romantic Weekend

Jennifer Frazer — Sun, 28 Feb 2010 16:28:23 +0000

I've been at an awesome wedding out of town this weekend, so here is a sweet treat that fits with that theme from the latest in our Pre-Life trailer series. The Fresh Prince called. He wants his haircut back. Grebes are interesting taxonomically. Originally, in the old system of classifying life whereby scientists squinted at creatures and lumped them with whoever they seemed to look most similar too (more or less), grebes were classifed with the similarly aquatic and water-dancing (and awesome-voiced) loons. However, there were doubters, including some wild-eyed crazies who, when they took a closer look at the details of grebe anatomy, determined they shared many unique characteristics (scientists would call them synapomorphies, which are the gold standard for modern evolution-based classification) with . . . are you ready for this? . . . flamingoes. Lo and behold, DNA comparisons bear this out. If that wasn't enough to convince you, it turns out that flamingo lice are actually closely related to grebe lice, seemingly having diverged only when the two lineages of bird split. So it seems the hypothetical grebe-loon connection was yet another case of convergent evolution, whereby unrelated organisms evolve to look similar when they set up shop in similar environments. This happens all the time and really messed with taxonomists until DNA sequencing came along. Here's a nice tree to give you a sense of who fits where; click "Podicipediformes" to take a closer look at the grebe family itself. Life is coming in March, my American friends with cable! Get excited!

wiki_bathyscaphe_trieste

Jennifer Frazer — Wed, 03 Mar 2010 03:14:07 +0000

wiki_HMSChallenger

Jennifer Frazer — Wed, 03 Mar 2010 03:16:40 +0000

The Oceanic X Prize: Deep Sea for the Rest of Us?

Jennifer Frazer — Wed, 03 Mar 2010 14:07:54 +0000

"This here's a bottomless pit, baby. Two and a half miles, straight down." -- Catfish De Vries, The Abyss One of my many dreams is to travel to the bottom of the ocean to see hydrothermal vent communities, bizarre abyssal creatures and methane seeps with my own eyes. I can't believe I missed this when it came out, but that dream took one giant leap forward in January: The X Prize people (of first private spaceflight fame) have announced a prize for the first company to return humans twice to Challenger Deep, the deepest point on Earth -- 35,761 feet down. That's over six and a half miles. In that crushing water, the pressure is 15,750 pounds per square inch: over 1,000 times atmospheric pressure at sea level. The announcement was made 50 years to the day after the first -- and still only -- two people reached that spot and returned alive. Above you see the Bathyscaphe Trieste, the first vessel to reach this spot, manned by Jacques Piccard and U.S. Navy Lieutenant Don Walsh on Jan. 23, 1960. An article in The Times of London announcing the X-Prize news describes the tense descent that, unlike Neil Armstrong's famous approach, has gone largely unheralded by history.

On a test dive off the island of Guam two months before the dive, the glue holding the hull together failed after the Trieste had just set a new record at 5.4km. Metal bands were used to strengthen it, and dives continued. On the big day, water began dripping into the cabin, but Jacques Piccard and Captain Walsh carried on and the leak stopped. Then, at 9.5 km, a crash shook the bathyscaphe. “In the past we had some very small external components fail and those events produced sharper sounds of implosions. This noise was much lower in pitch, as if something big had broken,” Captain Walsh told The Times this week. The two men checked their instruments. All seemed fine, so they continued. But a porthole on one of the tubes used to access the cabin had cracked. They were not in immediate danger, but if the tiny window gave way they would die instantly. “We could see it bulging, being pushed inwards by the pressure of the sea,” Captain Walsh said.

You can read the rest over at The Times. Though few people can recite the details of this dive or where they were when it happened the way most people know exactly what they did on July 20, 1969, the event and place have still crept into our culture. Auguste Piccard, father of Jacques and designer of the Bathyscaphe, and/or his brother Jean Felix inspired Gene Roddenberry to name his new starship captain Jean-Luc Picard. Challenger Deep itself is named after HMS Challenger, a sailing ship that led the first true oceanographic cruise of the world's waters from 1872-76 that is still renowned in scientific circles, cataloguing 4,700 new species and taking the first soundings of the Deep that bears its name. The expedition also inspired the naming of one other landmark exploratory vehicle -- the Space Shuttle Challenger. Yet in spite of the significance of this step, people have never returned to Challenger Deep. According to the Times, Piccard and Walsh fully expected it to happen in a few years with a better-designed sub. Instead, 50 years have passed. Only two remotely operated vehicles have returned. The X-Prize people, with any luck, will soon fix that. The Times expects ocean nuts and kajillionaires James Cameron of The Abyss, Titanic, and (I cringe to mention it) Avatar fame and Paul Allen of Microsoft to be contenders for the prize. And though they go with exploration and science on their mind, worthy ends by any measure, it bodes very well for me and any of you who've ever dreamed of exploring life in the deep. Right now, reaching the deep ocean in person is excruciatingly expensive and limited to a few lucky scientists and an occasionally extremely lucky member of the press. Even if the immediate aim is research and exploration, a successful design could be developed commercially by one of these guys to take the rest of us to the ocean floor much as X-Prize-Winner SpaceShip Two (aka Richard Branson's sexy new ride) will soon open the heavens to mere mortals. Well, mere mortals with 200 Large to spare. They say that fare might eventually come down to $10,000. I'd pay that to see any of this. Sir Richard thinks everyone should be able to experience space; I think everyone should be able to experience the ocean deep. I hope I'm not the only one.

flickr_lava_tube

Jennifer Frazer — Fri, 05 Mar 2010 19:36:10 +0000

Bacterially Tye-Dyed Caves

Jennifer Frazer — Fri, 05 Mar 2010 19:48:30 +0000

[caption id="attachment_2640" align="alignnone" width="597" caption="Lichens(?) and bacteria coat the interior of a lava tube in Hawaii. http://www.flickr.com/photos/lrargerich/ / CC BY 2.0"][/caption] Life on Earth is everywhere, from pores in rocks miles beneath the surface to tiny cloud particles floating high above. Here's another example of life turning up in a spot we'd not previously suspected: cave mineral deposits. Turns out the colorful encrustations are sometimes raw bacterial sewage. Pretty sewage, though! Cave bacteria are often actinomycetes, which were so named because they actually branch (yes, some bacteria can branch!) and make spores similar to fungi. They're also part of the crowd responsible for that wonderful earthy/cavey smell I mentioned a few posts ago. Actinomycetes are great at making competing-bacteria repellent, aka antibiotics. You might have heard of a few: actinomycin and streptomycin. This came out in November but I'd been saving this slide show for a fun Friday eye-candy treat. Enjoy!

Wiki_Deathvalleysky_nps_big

Jennifer Frazer — Wed, 10 Mar 2010 05:34:48 +0000

Giant Amoebae on (Extremely Slow) Rampage

Jennifer Frazer — Wed, 10 Mar 2010 07:00:19 +0000

This is so cool. I totally missed it when it came out in November 2008. If you did too, here's your second chance. In Russia, amoeba study YOU. OK, giant deep-sea amoebae that roll around like possessed dust bunnies? AWESOME. The 411. Though this group had just been discovered in the Arabian Sea in 2000, it seems it was still a surprise to find them *leaving tracks* (although I should emphasize no one can actually see them move in real time. This sounds like a job for the BBC's magic time-lapse camera). They are testate amoebae, or ameobae that make shells called tests (a few other deep sea protists like foraminifera also make shells called tests, and I just discovered that Chris Taylor over at Catalogue of Organisms just happens to have coincidentally published on the foram version yesterday.). This species, Gromia sphaerica, fits into the Gromiidea on this tree. Just look at all the uncharted territory and things you've never heard of. Space is not the final frontier. . . not by a long shot. Not yet. The bigger, non-motile existing deep-sea protozoans Matz refers to in the video are probably xenophyophores, an outrageously bizarre group alluded to here before. You'll just have to wait on a post about those another day. And there's probably lots more giant deep sea protists I don't know about yet. Readers? The big take-home message of Matz's discovery (or at least what they'd like us to take home) seems to be that we could really be misinterpreting Pre-Cambrian fossil trackwaves -- that is, the fossil tracks of organisms that predate the blossoming of most modern animal groups in an event called the Cambrian Explosion, ca. 550 million years ago. These tracks can be found in fossils as old as 1.8 billion years (yes, that's billion with a pinkie to the corner of the mouth). These tracks were for many years interpreted as early modern animals for whom we just didn't happen to have fossils. But what if they were giant protists? Or something else? Possible, and probably not surprising given the fossils we do have of Ediacaran creatures, they bizarre early animal(?) forms that predate the Cambrian explosion and are the first fossils of complex multicellular organisms we have. They all seem to be soft and, for lack of a better term, pillowy. Yes, like Charmin. Will we ever know? Probably not. But you never know. A fossil of a recognizable ancestor of a modern animal keeled over at the end of one of these tracks might settle things. On the other hand, simple tracks do tend to look alike. And with hundreds of millions of years on hand, there's plenty of time for lots of really weird things we'll never know about to have made them. You know what this video reminds me of, of course . . .

spiders-2658

Jennifer Frazer — Sat, 13 Mar 2010 16:10:23 +0000

Fig2_Nature_1Dec09_v2

Jennifer Frazer — Sat, 13 Mar 2010 16:41:12 +0000

The Creepy-Crawly Branch of the Family Tree

Jennifer Frazer — Sat, 13 Mar 2010 19:01:11 +0000

Arthropods! The prolific joint-legged and exoskeletoned group is up there with bacteria, archaea, and nematodes in the relentless numerical domination of Earth's surface. Here is a picture of me with one taken this week: It's a whip scorpion, in the order Thelyphonida, although this one has sadly somehow lost its long thin tail, or "whip" (called technically, like those of protists and sperm, a flagellum -- but they are *not* evolutionarily-related structures). This one seems to be very well fed, though thankfully not on Jen. I'm taking a short arachnology class at the Denver Museum of Nature and Science right now, and this was one of our subjects. According to my classmate, these animals, also commonly called vinegarroons because of the defensive acetic acid (vinegar) glands they possess near their tails, are the nerds of the arachnid world: "They just kind of bumble along, smelling like a salad." Raptoral pedipalps (big scary pincers) aside, the one I held did seem to be a sweet, gentle creature. I've now held a whip scorpion! Yay! I haven't talked about arthropods at this blog much yet, and a paper published in Nature a few weeks ago together with my play date with Stumpy, above, provide the perfect opportunity to correct that. This post is called "The Creepy-Crawly Branch of the Family Tree", but it could equally well be called the Floaty-Swimmy Branch, or the Bloody-Sucky Branch or the Borey-Eggs-Iny-that-Hatchy-and-Devour-the-Insides-of-your-Hosty Branch. There are arthropods that do all these things. So let's have a look at the broad shape of the tree as revealed by this new analysis of the evolutionary relationships among members of Arthropoda: [caption id="attachment_2670" align="alignnone" width="608" caption="Fig.2 from "Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences" Jerome C. Regier, Jeffrey W. Shultz, Andreas Zwick, April Hussey, Bernard Ball, Regina Wetzer, Joel W. Martin & Clifford W. Cunningham Nature 463, 1079-1083(25 February 2010) doi:10.1038/nature08742"][/caption] Now there are a lot of scary words on this diagram, it's true. But take heart! Look how many drawings of awesome creatures there are! And it's way better than the alternative that most biologists have to deal with, which I also had to learn to read in school. Before I get to what's new and cool about this tree, let's talk a little bit about what trees like this are, and then about the main groups you see on it. This tree is called a phylogeny, or phylogram (you also hear cladogram). It is a hypothesis of evolutionary history. That doesn't mean scientists are hypothesizing that these creatures evolved. That's a foregone conclusion. The hypothesis is what the specific relationships are between the different groups. In other words, the question is, "How is everyone related?", and this tree is one possible answer. In some trees, as appears to be the case here, the branch lengths are proportional to the evolutionary distance between the different groups. That is, the longer the branches, the more evolvin' that's been going on. Evolution, in this case, is measured in DNA nucleotide changes. DNA, as you'll recall, is made of many base pairs called nucleotides. There are four kinds. When one changes to another, that is called a point mutation. The more of these changes that build up, the greater the evolutionary distance between groups. For this tree, scientists studied 62 genes in 75 arthropod species. They sequenced them all and compared the changes. They put all the data into a special computer program designed to figure out which sequences are most similar to which other sequences in the five-jillion possible combinations of relationships embodied by 62 genes in 75 species. Then they cranked the computers up to 11 and probably waited a few days (or maybe even weeks! I have heard stories of scientists locking computers in closets during this time) for them to churn out the solution to this hyper-space chess problem. The lone tree you see above is the result. So what do we see? At the top is Hexapoda, which as you may guess are insects and friends -- the six-legged among us. Below them you see an interesting group called Xenocarida. More on them later. Below that group are the Vericrustacea and Oligostraca, which are both, as far as I can tell, basically crustaceans. In both groups you see some old friends: the copepods (some freshwater species of which carry Guinea Worm larvae, a topic I covered in January), the ostracods (who we looked at in a post on deep-sea bioluminscent organisms last year), and the Decapoda, which has a high taxonomic tastiness index: it includes lobsters, crayfish, crabs, and shrimp. Next are the myriapods: centipedes and millipedes. Below that are the chelicerates, or organisms with special mouthparts called chelicerae -- sea spiders (pynogonids), horseshoe crabs, scorpions, ticks, mites, tarantulas, spiders, and Stumpy. And rounding out the base of the tree are the outgroups -- the groups we use to "root" the tree, or give it a direction. They are usually the most closely related organisms not in the group of interest, here arthropods. In this case, they are the ridiculously cutely-named water bears or moss piglets -- the tardigrades -- and velvet worms, the onychophorans. Velvet worms are half of the subject of a crazy-*** theory that somehow got published last year hypothesizing that metamorphosing insects like butterflies were the result of an unholy chimerical union between velvet worms and a larva-less insect. Also looming large in the arthropods but not on the tree simply for reasons of chronological discrimination (and also because, being extinct, we have no DNA to sample) are the the trilobites. According to my copy of Colin Tudge's Variety of Life, they branched off somewhere between the Tardigrades and Chelicerates. OK, so now that you've waded through all of that, what were the surprises in this new tree? Scientists also used to think millipedes and centipedes were closely related to insects. They're both land arthropods, after all. My two college biology texts (published 1995 and 1996) show this relationship, though Tudge(2000) is agnostic on whether millipedes and centipedes or crustaceans are more closely related to Insects. Now it appears certain that, since all crustaceans are aquatic, insects and centipedes/millipedes represent a seperate evolutionary invasion of land by arthropods, much as seals and whales represent two seperate re-invasions of the sea by mammals. This study also supports the hypothesis that insects evolved from a crustacean, which is why we can't use the term "Crustacea" any more -- the group as traditonally defined doesn't include the insects, but this tree shows that it should (since the principles of modern evolution-based taxonomy require proper groups to include an ancestor and ALL of its descendants). The term "Reptiles" poses the same dilemma, because it should technically include birds. So some scientists have stopped using that term as a taxonomic classification, too. Little-r reptiles is OK, though, as informal name for the group. Finally, it appears hexapods' (insects') closest relatives are an obscure underwater-cave-dwelling group newly dubbed the Xenocarida. Carl Zimmer goes into that in admirable detail here. But the take-home message of this tree for you is simple: look, admire, and marvel at the variety and abundance. In fact, I give you a homework assignment, should you choose to accept it: pick a group on that tree that looks interesting that you've never heard of before. Look it up. Find out what it is, what it does for a living, and where it directs its mail. You'll be glad you did, I promise.

Late June 2009 065

Jennifer Frazer — Mon, 15 Mar 2010 04:21:12 +0000

Taking "Life" on the Road

Jennifer Frazer — Mon, 15 Mar 2010 13:43:01 +0000

[caption id="attachment_2692" align="alignnone" width="614" caption="Me and the state I love. Eccles Pass (12,435 ft) in the Gore Range, Colorado, July 3, 2009. Some of the meadows behind me were absolutely COATED with yellow glacier lilies. "][/caption] I've been thinking of what I can do to support this year's International Year of Biodiversity, and I've decided I'd like to take my "Life on Earth" lecture on the road. The talk will not be mere platitudes about biodiversity and its importance; we're talking specifics -- interesting science, weird organisms and their "alternative" lifestyles, beautiful photographs, and more natural history than you can shake a stick at. Basically, more of the same stuff you come to this blog for, plus you'd get to meet me and pick my brain in person. I'm planning to expand the 25 minute talk I gave last year at the Colorado Skepticamp into something closer to an hour (although half an hour is still an option) that I could give at a few venues around the Front Range (or perhaps farther afield if travel stipends are involved). If you are in a group that would be interested in hearing me talk on the subject of biodiversity and life on Earth, leave a comment to this post or contact me privately at the email address listed on the Portfolio page. I can't guarantee I'll be able to speak for everyone who makes a request (should there BE any requests : ) ), but all requests will be carefully considered.

wiki_campylobacter

Jennifer Frazer — Wed, 17 Mar 2010 02:55:21 +0000

wiki_Klebsiella_pneumoniae

Jennifer Frazer — Wed, 17 Mar 2010 03:56:13 +0000

The Biodiversity of Cigarettes

Jennifer Frazer — Wed, 17 Mar 2010 15:13:39 +0000

[caption id="attachment_2711" align="alignleft" width="450" caption="Campylobacter "twisted bacterium" sp. I need quotes around my middle name. Note the stringy flagella. U.S. Agricultural Research Service"][/caption] Not long after I became a health and environment reporter in Wyoming, I was assigned to cover a smokeless tobacco talk given by a scientist from the Mayo Clinic. Smokeless tobacco (aka moist tobacco, chewing tobacco, and spit tobacco), he said among other points, supported huge populations of live bacteria. That was surprising to me. I'd never thought about it before, but it did make sense. The tobacco companies don't exactly autoclave their product. Since it was my job to report on the talk, I reported that the substance was "teeming with bacteria", a statement I felt was amply supported by the evidence presented by this guy. The next day I got a call from a scientist at a state university in the south. He said he was calling to correct what he claimed were the inaccuracies in my story. He then proceeded to enumerate my alleged errors. I clearly remember him singling out the "teeming bacteria" statement. "Come on," he said. For those of you not in the United States, the Mayo Clinic is one of the top, if not the top, medical centers in the country. And though the Mayo Clinic scientist backed up my reporting on his talk when I subsequently called (and the story was just about his talk -- not an attempt at a broader survey of the science, even if the southern scientist's points had been backed up by a broader literature), I felt stung, to be sure. The Gulf Coast scientist even went so far as to send me some of his papers supposedly disproving what I'd written. It was all rather odd. I ask you, why would a scientist at a university 1,000 miles away go out of his way to call a reporter at a circulation 18,000 paper in Wyoming to correct alleged errors that in no way mentioned his research? How would he even know about the story? Well, guess what? It turns out that not only is smokeless tobacco teeming with live bacteria, so are dry cigarettes, according to a recent article in Science News (see also here for an earlier article). Scientists have found genetic markers for hundreds of species in cigarettes, and have cultured several of them out of packages purchased off the shelf. When cultured with blood, some of these bacteria can digest it. And as the article points out, scientists have long known smokers have higher rates of lung infection. Doctors always assumed that was due to immune system suppression. But inoculating your lungs with bacteria or their spores several times a day probably doesn't help. In retrospect, it's not surprising. You take leaves. You hang them up in a moist, dark, warm place (a tobacco barn). You wait. In plant pathology, we called this a moist chamber*. It's how we coaxed fungi to fruit so we could grab their spores for pure culture. Bacteria seem to like the treatment too: scientists found Campylobacter, Clostridium, Corynebacterium, Klebsiella, Staphylococcus, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, Escherischia coli, and Bacillus subtilis signatures in cigarette tobacco, according to the Science News article. Not only is this a who's who of the pathogenic human bacteria world (although is should be noted many species in these genera are not pathogens under ordinary circumstances), these and other bacteria are responsible for producing the most potent carcinogens in cigarette smoke -- nitrosamines -- when they start chowing down on tobacco leaves. Nor is this the first time cigarettes were found to be hosting . . . er . . . organisms. Cigarettes are often contaminated with plant viruses too. Though entirely harmless to humans, it's been known for years that people who've handled cigarette tobacco can transmit tobacco mosaic virus. Now don't get me wrong -- the presence of some bacteria is no reason not to eat or drink a food. Trust me, practically everything you put in your mouth has bacteria in it or on it. Even freshly cooked food probably has a few bacteria or fungal spores settle on it between the pot and your plate. And we purposely introduce billions of "good" bacteria and fungi into food all the time. If you've been reading this blog long enough, you know I'd be just as likely to say yogurt, your kitchen sponge, and your mouth are teeming with bacteria (which they are). This story does make me wonder, however, if tea leaves experience something similar to tobacco leaves during processing. Does anyone know? But you don't smoke tea, and the products of bacterial action on yogurt and tea leaves don't give people cancer. Tobacco bacteria do. Next time: a closer look at Klebsiella. ________________________________________________________ *Now that I think about it, I think we used grow lights over most of our moist chambers. But I don't think dark would necessarily discourage fungi.

Where There's Smoke, There's Klebsiella?

Jennifer Frazer — Fri, 19 Mar 2010 03:25:56 +0000

So who are the bacteria in cigarettes discussed in the last post? I don't have time to profile them all, so we'll briefly look at one I picked more or less because I didn't know anything about it: Klebsiella.

: Pink colonies of Klebsiella pneumoniae in culture. Brought to you by Pepto Bismol.

Klebsiella sp. are flagellum-less, rod-shaped, Gram-negative bacteria. The Gram state of a bacterium has to do with the properties of its outer coating; Gram-positive bacteria have a membrane surmounted by a thick outer wall made of peptidoglycan that readily takes up purple Gram stain, while Gram-negative bacteria have a thin peptidoglycan cell wall sandwiched between inner and outer membranes. Knowing the Gram-state of bacteria helps microbiologists sort out what kind of bacteria they might be dealing with. That's helpful, as you can imagine, when many of your subjects are simple balls (cocci) or rods (bacilli) that look more or less the same. The funny name comes from a 19th century German microbiologist named Edwin Klebs. The group is in the enteric bacteria, which itself is within the Gamma-purple bacteria. Misleadingly, many purple bacteria are not purple. But they are bacteria. Tricky, I know. That's probably why the group seems to have acquired a new name: Proteobacteria. See if you can find it on the bacterial family shrub. As implied by the term enteric bacteria, many are found in the gut of animals, but many others roam wild and free. Like Klebsiella, they're all Gram-negative rods, but some do have flagella. Enterobacteria contain some famous names indeed: Escherichia, Shigella(a maker of dysentery), Salmonella, Proteus, Klebsiella, Enterobacter, Erwinia(a plant pathogen that causes fire blight in apples and pears and soft rots in vegetable crispers around the world), and Yersinia, one species of which (Y. pestis) made it big as bubonic plague (aka The Black Death). There are others, too. Though Klebsiellas are sometimes human pathogens, some strains live happily in your gut or on your skin, and many others thrive in the environment and may never see a human their entire lives. There are presently about seven species of Klebsiella known, and they are becoming important as hospital-acquired (nosocomial) infections. Now we don't know what species was in the tobacco the researchers studied -- they only narrowed it to genus with their genetic screens. Perhaps many species in this genus were present. But take note of the final sentence from this WebMD article about Klebsiella pneumoniae:

Infection with Klebsiella organisms occurs in the lungs, where they cause destructive changes. Necrosis, inflammation, and hemorrhage occur within lung tissue, sometimes producing a thick, bloody, mucoid sputum described as currant jelly sputum. The illness typically affects middle-aged and older men with debilitating diseases such as alcoholism, diabetes, or chronic bronchopulmonary disease. This patient population is believed to have impaired respiratory host defenses. The organisms gain access after the host aspirates colonizing oropharyngeal microbes into the lower respiratory tract.

This Weekend: U.S. "Life" Premiere, and Going Off the Deep End in New Mexico

Jennifer Frazer — Sat, 20 Mar 2010 14:07:29 +0000

OK. This is it. Life premieres in America this weekend! For a video preview of the U.S. version (and in case you missed the huge banner ad splashed across the top of the NYT Friday, yet silly Discovery Channel still won't let me embed the video here), see here. For those of you with cable, rejoice. Deets: 8 p.m. Sunday, Eastern and Pacific. Perhaps 6 p.m. Mountain Time? For the rest of us; don't despair. That just means we'll get to see the original Attenborough version when it gets released to DVD, rather than the inferior Oprah-ized edition. Still, if I had cable, I'd be watching Sunday night. In other news, my car currently smells like the inside of a dive shop. Two gigantic neon tanks of compressed air (properly braced)? Check. Regulator? Check. 20 pounds of weights and weight belt? Check. Buoyancy Control Device (aka scuba life vest)? Check. Mask, fins, snorkel? Check, check, check. 7 mm wetsuit that adds the blubber equivalent (BE) of a pilot whale? Check. I've tried that puppy on, and all I can say is that there is clearly a reason sea creatures look doofy anytime they try to get around on land. This is about as thick as wet suits come, but in the Blue Hole (average temperature: 62-64F) where I'll be diving, I'll be glad to have it. 62F is trout country. Spirit of Adventure? Check. Remember when I discovered the Pelagic Magic blackwater dive? Well, I'm halfway to my dream. I finished the classroom and pool work for SCUBA certification in February, and this weekend I'm traveling to Santa Rosa, NM to complete my open water certification dives. My plane tickets are booked for Kona, Hawaii for April 17. I'm on my way. As for the rest of you, I want reports on the first episode of "Life"! I won't be around to post this weekend, so cozy up at home Sunday night for some Life on Earth goodness, and then report back here what you thought. See you next week!

Wiki_diatom

Jennifer Frazer — Tue, 23 Mar 2010 02:55:02 +0000

Microscopes + Victorians = Match Made in Heaven

Jennifer Frazer — Tue, 23 Mar 2010 03:01:20 +0000

[caption id="attachment_2787" align="alignnone" width="600" caption="Diatoms: the tinker toys of the microbial world. MacGyver could build a bomb out of the components on this slide. A modern microscopic image of diatoms, artfully arranged. Image by Wipeter, Creative Commons Attribution ShareAlike 3.0 License. Click for link."][/caption] There aren't many things about the Victorian world I would have liked, but their impulse to combine nature and art is one thing I could get solidly behind. Don't miss this slide show over at SEED Magazine highlighting the work of Victorian prepared slide makers. This was a time when the general public actually enjoyed scientific pursuits like looking at things under a microscope in their spare time, so much so that they could actually support an entire diatom art sweatshop industry. Seriously. It happened. Enjoy!

wiki_ct_quarter

Jennifer Frazer — Fri, 26 Mar 2010 03:01:32 +0000

flickr_plasmodium

Jennifer Frazer — Fri, 26 Mar 2010 03:02:18 +0000

The Math of Natural Beauty

Jennifer Frazer — Fri, 26 Mar 2010 03:26:08 +0000

Could not resist re-posting this short movie from Bioephemera lest anyone miss it. I love, love, love the music. I also love the way natural patterns are repetitive*. Similar patterns pop up in the oddest places. Look at the Charter Oak on the Connecticut quarter and you're looking at the search pattern of a feeding plasmodial slime mold (a giant ameoboid eukaryote), Physarum polycephalum, [caption id="attachment_2808" align="alignnone" width="603" caption="http://www.flickr.com/photos/randomtruth/ / CC BY-NC-SA 2.0"][/caption] which sends out protoplasmic veins in all directions in search of its prey: bacteria, fungal spores, and other microbes. Does math underlie that too? ____________________________________________________ *I also love how this video was for his mom. : )

Wiki_Diatoms2

Jennifer Frazer — Sun, 28 Mar 2010 19:52:37 +0000

Wiki-Diatom_biology

Jennifer Frazer — Sun, 28 Mar 2010 22:57:34 +0000

Wiki-Centric_diatom_life-cycle

Jennifer Frazer — Sun, 28 Mar 2010 23:11:10 +0000

Wiki-Diatom_pennate_life_cycle

Jennifer Frazer — Sun, 28 Mar 2010 23:18:06 +0000

Diatoms, or The Trouble With Life in Glass Houses

Jennifer Frazer — Mon, 29 Mar 2010 00:11:21 +0000

[caption id="attachment_2825" align="alignnone" width="603" caption="Diatoms: What would result if the Japanese could design their own microorganisms. These guys are screaming for a collector card set. Image by Rovag, Creative Commons Atribution 3.0 Unported License. Click for link."][/caption] Earlier this week I posted a link to Victorian microscope slides that included arranged diatom art. People really seemed to respond to the diatom image I posted with it, so I wanted to talk a little bit more about what diatoms are and a lot about their amazing shells. Diatoms literally live in glass houses, and as you can imagine, that makes sex, growth, and buoyancy a tricky business. How do you have sex when you live in the architectural equivalent of a microscopic petri dish? As they say -- very carefully.

A diatom is a single-celled organism that is also considered an alga -- for values of algae that include "anything that photosynthesizes(makes food using light) but isn't a plant or bacterium". They are in a high-level taxon called Stramenopiles, or Heterokonts, a group that's a grab bag of eukaryotic(cells with a nucleus) goodness that includes water molds (the oomycetes, a scion of which is responsible for the Irish Potato Famine), the fabulously cool and obscure slime nets (labrinthulids), and the brown algae. Here's the tree so you can see how everyone's related. Heterokonts are mostly algae, and the heterokontish algae are mostly diatoms. The name heterokont comes from the trait the group's common ancestor likely developed of having two unequal propulsive tails called tinsel and whiplash flagella (love the names!), though some groups (including the diatoms) have mostly lost theirs. Believe it or not, the tinsel flagellum (so called because of all the little hairs on it) actually points forward and pulls the cell through the water.

But enough about Heterokonts/Stramenopiles. Diatoms live in pretty much any moist environment, including mud puddles, wet rocks, film on moss, etc., though they are most commonly found in fresh and saltwater. If you've ever swallowed lake or seawater, odds are you consumed some unlucky diatoms.

Somewhere along the way, probably in the Triassic or early Jurassic, diatoms discovered that making their shells out of silica (SiO2, aka glass) instead of cellulose, chitin, calcium carbonate or any other mineral/molecule/protein/sugar saved them 8% in energy costs compared to an organic wall and helped them compete in a crowded phytoplankton marketplace. The glass shells of diatoms have an incredible structure: they come in two halves called frustules (again, love the name!) that fit together like a pill box. For you engineers and artists in the audience, here's your 1,000 words:

[caption id="attachment_2831" align="alignnone" width="491" caption="Schematic of diatom frustules. (A,B) Centric Diatoms. (A) girdle view, (B) valve view. (C,D,E) Pennate Diatom. (C) broad view, (D) valve view, (E) narrow girdle view (transverse section). Cupp, E.E. (1943). Marine Plankton Diatoms of the West Coast of North America. Bull. Scripps. Inst. Oceanogr. 5: 1-238 Image by Matt-eee, Creative Commons Attribution 3.0 Unported License. Click for link."][/caption]

As may be obvious, centric diatoms are radially symmetrical, and pennate diatoms are bilaterally symmetrical (like us). The valves are the face plates and the girdles are the sides.

Here's the problem with this system: when a diatom gets ready to divide, its shells pull apart and one goes with each daughter cell. Once these glass shells are formed, they can't really be . . . er . . . expanded. With glass, you get what you get. One of the daughter cells gets the big frustule or epitheca, and one gets the little frustule that fits in it -- the hypotheca. They both grow new shells that fit *inside* whatever shell they got. If you think about this, you'll realize that one of these two daughter cells got the raw end of the deal -- it can never get any bigger than its reduced-size shell. And one of its daughters will get an even rawer deal.

Carried out indefinitely, the cells keep dividing until they're so small they simply die. That does not sound like the recipe for an evolutionary WIN. Diatoms could, I suppose, get by on the part of their population that always inherits the biggest shell. But that's an increasingly small proportion of the population, and let's face it: after a while that frustrule is starting to seem a bit shabby, out-of date, and funny-smelling. So what is the escape from this evolutionary dead-end? I'm glad you asked!

Ta-Da!

[caption id="attachment_2832" align="alignnone" width="580" caption="Notice that the sperm have flagella that point *forward*. Those are the tinsel flagella, that pull the cell behind them. Image by Matt-eee, Creative Commons Attribution 3.0 Unported license"][/caption]

Sex! Sex is the answer! (I know what you're thinking: when is it not?) You have sex, grow your membrane out into a diatom shipyard, then build an entirely new and full-sized frustule inside. When you're finished, you simply cast off your old-and-busted frustules and membranes, and Voila! New Diatom hotness!

The above solution is what the centric, or radially-valved diatoms do. Here's what the rest of the diatoms do (warning: graphic diatom sex image):

[caption id="attachment_2833" align="alignnone" width="543" caption="Hey, baby, wanna swap nuclei? The life cycle of the pennate (not-radial) diatoms. Image by Matt, Creative Commons Attribution 3.0 Unported License. Click for link."][/caption]

Incidentally, like women of a certain age, diatoms also have a biological clock. If they miss their time to mate and make a new initial cell, they just keep dividing until they get so small they die all alone. Aww. Sad diatom.

So why do these utilitarian glass shells have all these beautiful shapes and forms? I wish I knew. What purpose natural selection has found in them I can't say, but I can say I appreciate the results -- and I'm glad I don't have to live in one.

june2008_cmsforay_jen

Jennifer Frazer — Tue, 30 Mar 2010 01:48:27 +0000

Mushrooms, Me, and You

Jennifer Frazer — Tue, 30 Mar 2010 02:33:05 +0000

[caption id="attachment_2865" align="alignleft" width="426" caption="Me and Ganoderma applanatum."][/caption] Mark your calendars -- I'm excited to announce I'll be teaching "Mushrooms of the Front Range" this August 19, 21, and Sep. 4 through the Boulder County Nature Association. If you are a fan of fungi or of just expanding your natural history world in general, come join us! The course description and instructions for signing up are here -- and the class size is capped at 12, so reserve your spot now. One of the things I enjoy most about mushroom hunting is the chance it gives me to *really* get to know the forest on an intimate basis -- not just the fungi, but also plants, animals, lichens, and whatevers -- and how the forest changes, and what grows where, and when. If you want to understand the part of life on Earth that takes place in a forest, picking up mushroom foraying as a hobby is a great way to do it. Plus you get to see some parts of your public land that almost no one else ever sees, and that's on top of all the bizarre things you find in the woods. Really, there are few nooks and crannies of forests near towns that haven't been touched by man, and that detritus is sometimes sad, sometimes fascinating, and sometimes utterly bizarre. And finally, it's so quiet and relaxing out there. If you like fishing, hiking, or meditation, you will love this. It's kind of a hybrid. With a nerdy basket. We'll be holding "Mushrooms of the Front Range" in August in Boulder just after the North American Mycological Association's 2010 annual meeting Aug. 12-15 at the YMCA of the Rockies' Snow Mountain Ranch over by Winter Park, so I will be freshly full of new fungal ideas and tales of Colorado fungi. Speaking of that meeting, you should come if you really want to immerse yourself in the world of fungi and perhaps equally eye-opening world of fungi-lovers, spend lots of quality time seeing beautiful views, get to know the Colorado sub-alpine forest post-mountain-pine-beetle (and I won't lie -- it's a tree graveyard in a lot of places out there), and hear all sorts of colorful lectures by world-renowned mycologists. It will be a ridiculously affordable natural history vacation: For about $300 (if you take a bunk in a room with five others and join the Colorado Mycological Society for a mere $28 or NAMA for $35/40) you can get all the fungal knowledge/foraying you can handle; all-you-can-eat buffet meals for breakfast, lunch and dinner; and lodging for three days. Trust me, as amazing science vacations go, this is dirt cheap, and it is going to be an awesome experience, even if it's a terrible mushroom year. And if it's a great mushroom year, the experience will be *unforgettable*. We may even be doing our third annual mycoblitz at Rocky Mountain National Park that week, which would allow you to take part in Citizen Science! One final note -- I have confirmed* a speaking engagement at the Denver Museum of Nature and Science for their November 3 Lunchtime Lecture series. The title has not yet been decided on, but the format will be a photographic survey of life on Earth that incorporates as much diversity as possible -- one beautifully photographed organism/phylum/minute for 45 minutes with a little bit of information about each. It will be less a science talk and more a science appreciation experience. Behold, and wonder. I'll have more information on it as the date gets closer. * Not so confirmed after all. Maybe not happening. : ( Stay tuned.

The Forests of Antarctica

Jennifer Frazer — Wed, 31 Mar 2010 01:17:15 +0000

Since this appears to be algae week here at The Artful Amoeba, I couldn't resist posting this video news from Antarctica: Hundred-foot tall forests of algae (in this case, kelp) in Antarctica?? Criminy! It's long been known that polar waters can be very productive where nutrients are brought to the surface by upwelling. But kelp forests? Which were formerly chiefly known (to the public) from California coastal waters? Cool! The kelp in the California version of these forests are known for their lightning-fast growth, in which they can solder on up to a foot and a half of new algae per day, reaching over 100 foot in length. Sea urchins then delight in chewing these things off at the root, setting the mighty fronds adrift after all that hard work. Whether they're capable of those growth rates in the bone- and cell wall-chilling waters of Antarctica, I have no idea. Though I'm sure the algae would love to have heater packs for their blades (can't call them leaves -- only plants have leaves), too. : ) These specimens appear to be brown algae (Class Phaeophyceae), again in the Heterokonts/Stramenopiles, with the tinsel and whiplash flagella on their mobile cells we discussed two posts ago. Brown algae get their characteristic color from one of their photosynthetic pigments -- fucoxanthin -- though they also possess chlorophylls a and c (true plants have chlorophyll a and b). They also serve as proof that some protists can form complex multicellular organisms. Though they don't have true roots, leaves, or vascular tissue(as far as I know) like "real" plants, they do have groups of specialized cells (aka tissues) like us "higher" animals, plants, and fungi. Though if you think about it, we all descended from protists at some point, so it should be no surprise. Social cell collectives (aka multicellular organisms) probably evolved many times from loner cells, though whether they all eventually go on to drop out of the ecosystem, grow their flagella out, and hang Grateful Dead posters everywhere is still a question for science.

The Amoeba Crawls this Weekend!

Jennifer Frazer — Fri, 02 Apr 2010 16:02:06 +0000

If all goes according to plan, this website will be making its move this weekend from frazer.northerncoloradogrotto.com to being truly hosted at theartfulamoeba.com (right now I employ masking to make that work). That may mean the feed will change and you will need to resubscribe, but I'm not certain yet as I have yet to consult with my volunteer tech department. Rest assured I'll do my best to make the transition as seamless as possible, and the feed may not need any updating on your end at all. If for some reason it does stop working, just go to theartfulamoeba.com and hit the little orange RSS feed subscribe button at the upper right to resubscribe this blog to your feed reader. In addition, if you have any links to my blog on your site, the links will break unless you sub theartfulamoeba.com for frazer.northerncolorado.grotto in the root once the transition happens. Finally, if you have a link to this blog in general from your blogroll, etc .(thank you! Very honored by that!), make sure the link is to theartfulamoeba.com and not frazer.northerncoloradogrotto.com I'm making this move to make things less confusing for readers (what the heck is frazer.northerncoloradogrotto.com?!) and in preparation for some big changes: I hope to attempt join to the Nature Blog network and Researchblogging.org soon and I figured it would be best to get the tech stuff squared away before I complicate things further. In any case, theartfulamoeba.com, artfulamoeba.com, theartfulamoeba.org, etc., will all continue working no matter what happens. Bear with me, faithful readers, and in the meantime, enjoy this movie of an amoeba strutting its stuff. This phenomenon by which amoebae move is called "cytoplasmic streaming". I love that the amoeba seems to "change its mind" several times about whether that top pseudopod (arm) should be expanding or contracting. : )

wiki_vanilla_planifolia

Jennifer Frazer — Sat, 03 Apr 2010 23:15:37 +0000

When the Pen is Mighter than the Lens

Jennifer Frazer — Sat, 03 Apr 2010 23:38:15 +0000

The host site transfer of this blog has been postponed until tomorrow. So in the mean time, let's look at some beautiful images of plants to celebrate this glorious spring weekend! Seed Magazine has created another gorgeous slideshow of biological art, this time highlighting the release of a new book on botanical illustration at the Kew Gardens called "The Art of Plant Evolution". In this new book, not only is art gorgeous and the plants (as ever) fantastic, the works are organized according to currently accepted evolutionary order. Useful! Educational! The book highlights modern examples of botanical art created after the advent of the camera. Though some may argue that instrument made natural history art obsolete, I beg to differ. Often art can highlight features that would be quite difficult to see in one photograph. Anyone who disagrees is directed to the Sibley Guide to Birds. Any guesses what the work above is of? It's something you use a lot . . . Think . . . don't peek till you've really thought about it . . . Vanilla planifolia is its name. Dairy flavoring is its game. When the long skinny fruit (packed with jillions of tiny seeds) turns brown and is properly cured and subjected to alcohol extraction, you end up with a dark brown liquor that little kids are always surprised to find tastes wretched. That's why you've got to add the products of Saccharum sp. and Bos primigenius. The plant is in the massive orchid family(Orchidaceae), one of the coolest on the planet. Its members generally live in trees and require particular symbiotic fungi to infect and feed their endosperm-less seeds before they can germinate, and they're known for producing exquisite flowers pollinated by a variety of specialized insects. Orchids have gone as far as tricking insects into having sex with their flowers so they can . . . have sex. Oh, the irony.