biodiversity – The Artful Amoeba http://theartfulamoeba.com A blog about the weird wonderfulness of life on Earth Tue, 11 Mar 2014 16:22:24 +0000 en-US hourly 1 https://wordpress.org/?v=4.5.31 All Mushrooms Bright and Submersible http://theartfulamoeba.com/2011/05/30/all-mushrooms-bright-and-submersible/ http://theartfulamoeba.com/2011/05/30/all-mushrooms-bright-and-submersible/#respond Mon, 30 May 2011 23:59:32 +0000 http://theartfulamoeba.com/?p=4993 Last week the International Institute for Species Exploration at Arizona State University released their list of the top 10 new species of 2010, which Nat Geo covered admirably here and is well worth a look. On that list was a mushroom I covered here last year, Psathyrella aquatica, the “Mushroom that Sleeps with the Fishes”.

What I did not know about then, and have just discovered, is that this mushroom doesn’t merely lounge around in quiet pools. It stands up to stiff currents, as seen in this amazing video I found at the ASU site.

Both the Nat Geo article and the ASU page contained some other gems. The caption to the glowing mushrooms in the Nat Geo article noted

San Francisco State University’s Dennis Desjardin and colleagues scouted for glow-in-the-dark mushrooms during new moons, in rain forests so dark the researchers often couldn’t see their hands in front of their faces, Desjardin told National Geographic News in 2009.

Ummm  . . . have you seen many of the things that live in rainforests? Walking through them in pitch black sounds like a Herculean feat of will, and hands-down one of the most bad-*** things I have ever heard of any scientist doing (although the guy who set out to sample the stings of every venomous insect and rate them on a scale of pain comes close). I give a Pseudopod Salute to these guys for courage in the line of duty. And it seems to have paid off, too.

But “when you look down at the ground, it’s like looking up at the sky,” Desjardin said. “Every little ‘star’ was a little mushroom—it was just fantastic.”

WOW. Witnessing for the first time a few hours of profound biological beauty sounds like it could well make up for the seriously high sphincter factor of this study. Like when Edith Widder turned off the dive lights on her autonomous diving suit 880 feet below the Santa Barbara Channel, or when I jumped into the North Pacific at night in shark-infested waters to see the nightly ascent of the bizarre pelagic biota. Sometimes, the payoff is worth the bone-quaking fear.

In the ASU description of the dentally-well-endowed but reproductively less blessed T. rex leech, known for teeth “that the leech uses to saw into the tissues of mammals’ orifices, including eyes, urethras, rectums, and vaginas,” (oh dear LORD) according to Nat Geo, was casually dropped this detail

This T. rex leech was discovered feeding from the nasal mucous membrane of a little girl in Perú.

Eeeeeeeeeee! Nat Geo did not mention it was a human parasite too!

And finally, in the caption for the Darwin’s Bark Spider at ASU, hidden amongst some other more or less routine description of a spider that spins gigantic webs was this

This orb-weaving spider builds the largest orb-style webs that are known to science.  Webs of this species have been found spanning rivers, streams and lakes with “bridgelines” reaching up to 25m in length and total web size reaching up to 2.8m2.  The silk spun by these spiders has an average toughness of 250MJ/m3 with the highest measured at 520MJ/ m3.  This makes it, “the toughest biological material ever studied, over ten times stronger than a similarly-sized piece of Kevlar” and more than two times stronger than any other known spider silk. The unusual behaviors of this new species will allow us to understand size dimorphism, mate guarding, and self castration (among others).

Wait . . . what was that last one?

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The 5-Million Year All-You-Can-Eat Buffet http://theartfulamoeba.com/2011/05/12/the-5-million-year-all-you-can-eat-buffet/ http://theartfulamoeba.com/2011/05/12/the-5-million-year-all-you-can-eat-buffet/#comments Thu, 12 May 2011 14:20:08 +0000 http://theartfulamoeba.com/?p=4833

Algae having a par-tay today. It's nothing compared to the 5-million year bender they went on 250 million years ago. Creative Commons eutrophication&hypoxia

This post was chosen as an Editor's Selection for ResearchBlogging.orgAbout 250 million years ago in what is today the vast backwater of north central Siberia, the Earth coughed forth an unimaginable quantity of lava over the course of 1 million years. The liquid rock was a low-viscosity, thin stuff (for lava), so instead of forming a field of towering volcanoes it oozed out into endless plains. Covering some 1.5 million square kilometers today (600,000 square miles — something like the surface area of Europe), the beds may have originally covered 7 million square kilometers and taken up 1 to 4 million cubic kilometers in volume.

Scientists still do not agree why this happened, although it has happened many times before and since around the world. But they do agree on the timing: it happened at the same time as the Great Dying — during the Permo-Triassic extinction just prior to the age of dinosaurs that wiped out more life on Earth than any other, including the one with the giant asteroid with our name on it.

Not all scientists agree that the Siberan Traps, as they are called (trap comes from the Swedish word for “stairs”, which is how the frozen lavas can appear today) chiefly caused the extinctions. But many do, and it seems to be solidifying (er, pardon the pun) as the majority opinion.

What is also known is that life took some time to recover from this cataclysm. For at least 5 million years after, we can find little in the fossil record. Scientists have wondered whether this was a case of too much or too little food.

How, you might ask, could too much be a problem? Well, visit your nearest pond contaminated by fertilizers from lawns, golf courses, or farms and you will see: vast swarms of algae, that hog all the oxygen and choke out “higher” forms of life like fish. Or, for that matter, the New-Jersey-sized Dead Zone in the Gulf of Mexico, which formed in response to the endless streams of fertilizer runoff from farms pumped into the sea by the Missouri, Mississippi, and Ohio River system. We call this eutrophication*, and now, the authors of a paper in in Earth and Planetary Science Letters are pretty sure it is what prevented most life from recovering for those five million long years.

What happens when the party gets a little too wild. A lake in China with rampant eutrophication. Creative Commons eutrophication&hypoxia

How might scientists figure this out? As it turns out, one of the enzymes that catalyzes photosynthesis has a quirk. Thinking back to high-school chemistry, recall that the nucleus of an atom is made of protons and neutrons. Different elements are defined by the number of protons their nuclei contain. Carbon *always* has six protons. If it had seven, it would be nitrogen. But elements can vary in the number of neutrons they have. Carbon, for instance, can commonly have six neutrons or seven. Carbon-12 represents the former, while carbon-13 the latter.

As it happens, one of the chief enzymes of photosynthesis — RuBisCO, the one responsible for grabbing carbon dioxide from air and setting it on the path to become glucose — processes carbon dioxide containing carbon-12 a little faster than carbon dioxide containing carbon-13. Over jillions of cycles, the difference accumulates, and life becomes enriched in carbon-12. It makes little or no difference to the organisms themselves.

But it makes a big difference to scientists, who can use this knowledge to tell how fast the oceanic biological pump — the transfer of carbon from the atmosphere and surface waters to the seabed by microorganisms that live, die, and sink — is churning. The more these microbes nom, the more carbon-12 builds up in preference to carbon-13 in seabed deposits, where marine algae sink, store carbon, and are eventually pressed into limestone after they die. Scientists who studied marine deposits recorded in Chinese rocks during this 5-million year gap have found the carbon-12 enrichment is about double what exists today. If life had starved after the Traps did their dirty work, they would expect to see the opposite.

This is the scenario the authors of this new paper believe may have happened: as they erupted, the Siberian Trap lavas and the rocks they metamorphosed by contact spewed carbon dioxide (as well as many other volcanic gases) into the atmosphere. This warmed the atmosphere, which increased the evaporation of water, itself a greenhouse gas, perpetuating the cycle.

At the same time, more water vapor produced more rain, which weathered the land quickly. All that runoff drove incredible quantities of phosphate — a nutrient that limits the rate at which marine algae can grow — into the ocean. With a new all-you-can-eat buffet of phosphate and carbon dioxide at their disposal, marine microbes went nuts. The ocean was stripped of free oxygen, preventing any animal life that had managed to survive the extinction itself from regaining ground. Once the initial trauma of the Permo-Triassic extinction was over, these algae must have bloomed in quantities unimaginable. What is now the Blue Planet, and once may have been the White Planet, was briefly, it seems, the Green Planet.

What finally stopped the madness (from our perspective as vertebrates), was the waning of the volcanoes. Eventually, carbon dioxide levels dropped, and warming and rainfall decreased. With less erosion, oceanic phosphate and nitrogen concentrations dropped. Without enough of these nutrients to go around, algal numbers shrank, leaving enough oxygen around for other forms of life to exploit. And, luckily for us, they did.
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* Which is the reason you should all be using phosphate-free detergents.
ResearchBlogging.org
Meyer, K., Yu, M., Jost, A., Kelley, B., & Payne, J. (2011). δ13C evidence that high primary productivity delayed recovery from end-Permian mass extinction Earth and Planetary Science Letters, 302 (3-4), 378-384 DOI: 10.1016/j.epsl.2010.12.033

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The Many Ways to Be a Fungus (in Colorado) http://theartfulamoeba.com/2011/04/16/the-many-ways-to-be-a-fungus-in-colorado-2/ http://theartfulamoeba.com/2011/04/16/the-many-ways-to-be-a-fungus-in-colorado-2/#respond Sat, 16 Apr 2011 18:38:28 +0000 http://theartfulamoeba.com/?p=4681 At last, here’s a recording of the 45-minute lecture I gave in March to the Colorado Mycological Society: The Many Ways to Be a Fungus (in Colorado). The lecture discusses fungal diversity using Colorado examples, but it should be interesting to anyone who wants to learn more about fungi. I hope to have a full post ready for you early next week. In the meantime, enjoy!

The Many Ways to Be a Fungus (in Colorado) from Jennifer Frazer on Vimeo.

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Empire of Light http://theartfulamoeba.com/2011/03/03/empire-of-light/ http://theartfulamoeba.com/2011/03/03/empire-of-light/#comments Thu, 03 Mar 2011 21:52:26 +0000 http://theartfulamoeba.com/?p=4324 “His only hope for existence on this planet is as a gigolo. He’s gotta find himself a babe, and then he’s gotta latch on for life.”

I missed Edith Widder’s TED talk on ocean bioluminescence when it came out in 2010. Had I known, you would have been seeing this much sooner. It clocks in at 17 minutes, but don’t let that intimidate you; it speeds by. There’s a little something here for the biophiles, engineers, and daring explorers in all of us.

For a high-res version of this video, click here.

What I would have given to have been in that Wasp suit when she turned the lights out.

That jellyfish burglar alarm is just fantastically beautiful. Notice how the pattern is slightly different with each rotation. Why does it remind me of an ’80s electronic toy?

For the record, I am so with Edith on the whole, “When someone offers you a trip to the deep sea, you say YES.” In fact, I’m actively looking for a low-budget ticket to several thousand clicks down; it’s a dream of mine. I’m no Dennis Tito, but I can write. If you know someone traveling to the deep sea who might be in need of a science writer specializing in biodiversity and natural history who doesn’t eat much and fits conveniently in most overhead bins (5’2″, 108 lb.), LET ME KNOW.  : )

For a more in-depth look at deep sea life which Dr. Widder helped work on, see the Deep Sea episode of Blue Planet, available through netflix in the US (and mercifully narrated by David Attenborough, and not Oprah). You will not regret it.

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What’s in a Cubic Foot of Rainforest? http://theartfulamoeba.com/2011/02/28/whats-in-a-cubic-foot-of-rainforest/ http://theartfulamoeba.com/2011/02/28/whats-in-a-cubic-foot-of-rainforest/#respond Mon, 28 Feb 2011 15:55:48 +0000 http://theartfulamoeba.com/?p=4315

Rainforest on Mo'orea. Whatever you do, don't drop your keys in here. Creative Commons Tim Waters

National Geographic sent a photographer into the field to photograph every species he could find in a cubic foot of rainforest on the French Polynesian island of Mo’orea. It’s both an interesting illustration of some biodiversity (what about the microbes?) and a fun visual treat — take some time to just flip through the photographs and absorb the information visually. Don’t bother reading the scientific names (unless you must) — just read the common names, or just look at the pictures. Note the variations in shape and form.

I think they were looking much harder for insects than they were for fungi. I find it hard to believe they couldn’t find more — especially the little ones that like to hang out on rotting pieces of wood. Also: could we get a species ID on the lichen? Even to genus? A little respect, please!

In particular, notice how even otherwise dull-looking insects can have their special own beauty when viewed up close: the graceful sweep of the almond moth’s antennae, for instance, the fan dancer’s wings of the white plume moth, or the kinked wingtips of one of the kindeid moths. Other details to look for: Notice the antennae located on the snout of the weevil, and the ubercute juvenile Gump’s woodlouse. Awwww. Happy Monday, y’all.

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Earth’s Real Lost World — and its Imminent Entry http://theartfulamoeba.com/2011/01/13/earths-real-lost-world-and-its-imminent-entry/ http://theartfulamoeba.com/2011/01/13/earths-real-lost-world-and-its-imminent-entry/#comments Fri, 14 Jan 2011 01:45:37 +0000 http://theartfulamoeba.com/?p=4084

The warren of lakes beneath the Antarctic Ice Sheet. Zina Deretsky/NSF

Far more exciting to me than the (in my opinion) remote possibility of life on other worlds in our solar system is the near-guarantee of the discovery of unique life that could happen within weeks right here on Earth. For hidden beneath the thick layer-caked ice sheet of Antarctica is a lacy web of lakes that have been sealed in for perhaps 15 million years. And soon — perhaps this month — Russian scientists will breach the last veil of ice blocking our view of the biggest: Lake Vostok. The titanic lake — roughly the size of Lake Ontario and with a maximum depth double that of Lake Superior (2600 ft. vs. 1300 ft) and discovered only in the 1970s — lies under two and a half miles of ice.

Since there is virtually nowhere on Earth that life doesn’t thrive, I fully expect scientists will find it there. And it may be life that is unlike any other we have seen. We’re not just talking weird bacteria (although that would be AWESOME). There could be blind, bizarre fish, or other large organisms beyond our wildest imagination (although, it must be said, we have no evidence (so far) of a large energy source for the lake, so microbes might be it). Use your imagination — until they break through, you can imagine anything you want down there — trilobites, krakens (per one New Scientist reader), Nessie. THIS is incredibly exciting news.

There are several reasons to think the life in Antarctica’s Lake Vostok (Russian for “East”) might be seriously unusual and wonderful. First, it hasn’t been touched by humans. There was very little you could say that for even before the Age of Discovery — humans had touched nearly every terrestrial corner of the planet. You could make a good argument for many cave ecosystems where humans did not tread until this century. And they have unique life aplenty, but they also have water, life, and even pollution that percolate in from the surface on a regular basis, even where no (wo)man has set a foot. Not these lakes. To the best of our knowledge, they have been sealed to the outside since the ice sheets formed.

Second, the water of Lake Vostok is unlike water in virtually any other spot on Earth. It’s under enormous pressure thanks to jillions of tons of ice, and as a result, is super-oxygenated. We’re talking oxygen concentrations 50 times that of your backyard pond. And it must be said that oxygen is not the nicest of molecules from life’s perspective. Although properly harnessed, it’s a great power source, it’s also a bit like rocket fuel: volatile and reactive. Oxygen breakdown products called free radicals are like molecular loose cannons: capable of wreaking  havoc on DNA and other important cell bits. Accepting oxygen into your life (some bacteria — obligate anaerobes — refuse to do so and will die if they come into contact with the stuff) comes with a lot of extra wear and tear on the ol’ cell. So dealing with oxygen concentrations this high must involve some incredible cellular defense weaponry.

In addition, some of the embarassment of oxygen is believed to be tied up in clathrates — slushy mixtures of water and gas at the bottom of the lake. As you may imagine, popping the top on this baby could involve a reaction not unlike opening a 2-liter that has had a fun night with a paint mixer. More on that later.

Finally, although it is little-known today (I once had a senior scientist who shall remain nameless accuse me of making this up), Earth’s poles have on many occasions in its past — some quite recent — been lush and green. They were sub-tropical forests that somehow — I have no idea how — managed to survive three to six months of darkness each year. What subtropical forests and animals did under such circumstances is fascinating to think about. But we have abundant evidence of this — like petrified wood and tree mummies found on Axel Heiberg Island or more recently on Ellesmere Island in Canada (global warming is outing them). And here’s the thing: Lake Vostok was a lake before Antarctica was covered in ice. It was a lake during Antarctica’s Life o’ Riley. And its depths could well preserve evidence of that life, protected from the inexorable grinding crush of the overlying ice. WOW.

So there are many reasons to be excited about the exploration of Lake Vostok, provided we don’t somehow accidentally and catastrophically pollute or kill everything off by contaminating it with stuff from the surface. That, as always, is the trick. And it’s something scientists have been thinking about. How do you penetrate and explore such a place without destroying the very thing you came to study?

Good question.

Artist's conception of the drilling of Lake Vostok. For a more accurate view, visit the New Scientist article linked at the beginning of this post. Nicolle Rager-Fuller/NSF

The Russians have been working on this problem for well over a decade. Previous attempts to penetrate the lake were put on hold until Antarctica’s governing body could be satisfied they had a good plan in place to protect it. So the Russians halted with about 100 meters to go. As the wikipedia article mildly puts it:

This was to prevent contamination of the lake from the 60 ton column of freon and aviation fuel Russian scientists filled it with to prevent it from freezing over.

I gotta hand it to the Russians — no half measures for them*. Still, as may be imagined, a 60-ton column of freon and aviation fuel might not be the best way to introduce ourselves to the Lake Vostok locals. So they have a plan for this too.

According to New Scientist:

“Beginning late December, we will first use a mechanical drill and the usual kerosene-freon to reach 3725 metres. Then, a newly developed thermal drill head, using a clean silicon-oil fluid and equipped with a camera, will go through the last 20 to 30 metres of ice.”

Then, if all goes as planned, the lake will burst from its icy prison, freezing shortly into its trip up the borehole, plugging it. In theory, the borehole’s negative pressure should prevent any contamination from our end reaching their end. And then, sometime next year after the plug is good and frozen, we’ll bore into the newly frozen lake water. Our sample will be complete and the lake contamination free — we hope. Anyone who’s picked up a sci-fi novel (or a newspaper, for that matter) knows these things can go horribly wrong (for instance — let’s hope that ice-water boundary is not 20 to 30 meters higher than they think it is) — but to never look in the lake seems a mistake too. So bottom’s up, boys.

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*especially considering my solution to this problem would essentially be something like: get iron with really long cord. Set to “Linen”. Place on ice. Wait.

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Marine Census Illustrated http://theartfulamoeba.com/2011/01/07/marine-census-illustrated/ http://theartfulamoeba.com/2011/01/07/marine-census-illustrated/#comments Fri, 07 Jan 2011 16:33:22 +0000 http://theartfulamoeba.com/?p=4062

Myzostoma cirrifera. Upper layer of internal organs on the right, lower level at left. More on this guy below. Creative Commons W. Blaxland Benham (after Lang and von Graf)

As we ended last year with a slide show, so shall we begin this year with another. The Census of Marine Life has been a herculean 10-year mission to seek out new life and new civilizations (OK, maybe just one of those) in the ocean. The hundreds of scientists involved have succeeded spectacularly, though still have likely only scratched the surface.

Last fall scientists disclosed many of their results, and some of the most striking images have been collected by National Geographic into a tome called “Citizens of the Sea“, available since last fall. Cornelia Dean (science reporter and former science editor at the New York Times, who I was fortunate enough to meet in grad school (for science writing)) reviewed the book in the Science Times on Tuesday, and included a spectacular slide show that is above all what I’d like you to look at today.

But before I write more about that, my first impression of the book from flipping through it on Amazon is that it is curiously out-dated graphically. Its chunky photo layout and washed-out art seem like something you’d find in a National Geographic book from the 1980s. It pales in comparison to the stunning layouts and vivid photography of the University of Chicago Press’s “The Deep” and DK Books’ “Reef” and “Prehistoric Life”. The book also seems heavily weighted (as most are) toward metazoans, or, to put in in English, the big stuff in the ocean. As usual, microbes, protists, and larvae are missing out of proportion to their importance.

Of course, that has no bearing on the text, which I have not had time to peruse, and seems it may be more substantial than what you get in those other books since it was penned by Nancy Knowlton, a marine biologist at the Smithsonian. And judging by the nine five-star reviews at Amazon (the book received no ratings less than five), the writing is where the book shines, just as much as it is wanting in those other books.

Still, as Ms. Dean points out, the book is a bit scattershot taxonomically, making it hard for readers to understand biodiversity systematically. That omission — common to many books — is part of why I started this blog. When you can fit new organisms into general taxonomic groups in your head and relate them to other groups, it not only makes organisms easier to remember and their biology more understandable, it helps you understand the path of evolution too.

OK, back to what really matters: the critters. A few comments on the organisms in the slide show: When I was in grad school (for mycology), I studied fungal spores that, while admittedly huge for fungi, were on the order of the same length as the copepod (Ceraqtonotus steinigeri) pictured in the show — 200-300 micrometers (not my spore photo, but take a look here). That’s right: there are fungal spores as big as that copepod, which looks like it could be shrimp-sized if you didn’t have the scale bar to tell you better. Think about that.

You’ll also notice that the show features two — countem, 2! — new Arctic bryozoan species. Remember the bryozoans — the moss animals? I covered them in my first guest blog at Scientific American. The photographs are of their calcareous skeletons only — the little animals you’d find poking their lophophores (crown of feeding tentacles) out of those holes are conspicuously absent, probably due to the preparation method involved in scanning electron microscopy — that is, spraying your sample with a film of gold.

Finally, I want to point out a delightful little organism new to me — the myzostomid, or parasite of crinoids, or sea lillies near the end of the show (see additional illustration at top of this post). I could write a whole book about the sea lillies and their charms (they were super-abundant in former times, and their fossils are still so. You can find little stem pieces in marine rocks all over North America, and the most stunning collections of fossilized sea-lily beds are swirling virtuoso works of Art Nouveau). But this little guy (being unceremoniously trod upon by a limelight-hogging shrimp) is apparently a representative of an entire group that has evolved just to parasitize sea lillies*. The myzostomids, while unrelated taxonomically, seem to be part flatworm (their diverticulated reproductive system resembles the dendritic digestive system of flatworms), part chiton/scale insect (their shield-like bodies). They’ve even adopted the vivid coloration of their hosts.

And here’s the kicker: they’re annelids — the group traditionally known as “segmented worms”, the most famous member being the humble earthworm. You see the segments? Me neither. Evolution: the great aimless wanderer. But oh, what beauties it stumbles into.

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*They’re active feeders on sea lillies, so I don’t know why the slide show caption says that it’s “commensal”, or a passive guest. Of course, Cornelia also says that the tubular eyes of the barreleye fish stick up above its head, when, as expertly covered by Steven Colbert two years ago, they are clearly inside its see-through head. Don’t get too mad at Cornelia, though. As a former reporter, I can say we do our best, but we’re on deadline, and sometimes we make mistakes.

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Attention Female Slugs: Beware Ninjas Bearing “Gifts” http://theartfulamoeba.com/2010/12/30/attention-female-slugs-beware-ninjas-bearing-love-darts/ http://theartfulamoeba.com/2010/12/30/attention-female-slugs-beware-ninjas-bearing-love-darts/#comments Thu, 30 Dec 2010 17:29:03 +0000 http://theartfulamoeba.com/?p=4052

This is *not* the ninja slug, but if you imagine that seedpod is a katana, we're 90% of the way there. OK, maybe not. Creative Commons papalars. Click for link.

As the year rounds down, I wanted to point you in the direction of a nice gallery put together by the editors at National Geographic of 2010’s weirdest new animals.

My fave: the ninja slug of Borneo. Apparently these guys shoot calcium carbonate hormone-soaked “love darts” into their paramours. Somehow this increases reproductive fitness, though whether it does so by helping lady slugs make more eggs or by putting them more “in the mood”, if you know what I mean, Nat Geo does not say. The wikipedia page seems to imply love dart hormones increase sperm survival on the part of the shooter, and that the use of the darts is fairly widespread among land snails and slugs. As with so many invetebrate systems, I’m *really glad* this is not a part of human courtship. Do not miss the gallery of love dart photos and drawings at the bottom of the page — fascinating. On a related note, anyone who has not scene the epic snail love scene (complete with opera music) in “Microcosmos” is greatly missing out. The snails look like they’re having more fun than most humans. Run, do not walk.

Taxonomically, slugs are snails that lost their shells. Like lichenization, this turn of events has taken place many times in unrelated groups, so “slugs” are what taxonomists call “polyphyletic”, or not a true, valid taxonomic group (which should always be based on a single ancestor and its descendants — that is, a monophyletic group). There are even some slugs that are still in the process of losing their shells and carry a tiny shell too small to duck into on their back, rendering them “semi-slugs”. Slugs are gastropods, which are in turn molluscs. You can see how it all fits together and who else they’re related to here. That’s it for 2010! See you in the New Year!

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Of Arsenic, Slime Molds, and Life on Other Worlds http://theartfulamoeba.com/2010/12/09/of-arsenic-slime-molds-and-life-on-other-worlds/ http://theartfulamoeba.com/2010/12/09/of-arsenic-slime-molds-and-life-on-other-worlds/#comments Thu, 09 Dec 2010 15:53:50 +0000 http://theartfulamoeba.com/?p=3971 I have kept silent on last week’s announced discovery of bacteria from Mono Lake, California, alleged to be able to grow using arsenic instead of phosphorus — until now. I was reading a news analysis on the subject of the improved odds for life given this and other recent discoveries in biology and astronomy in my morning paper and stumbled on this intriguing allegation:

Another reason not to get too excited is that the search for life starts small – microscopically small – and then looks to evolution for more. The first signs of life elsewhere are more likely to be closer to slime mold than to ET. It can evolve from there.

I’m not sure whether to take that as in insult to an incredibly evolved and highly complex life form or not. Hey — how many protists do *you* know that can learn to anticipate regularly timed stimuli, drive robots, solve mazes, and plan high-speed rail routes? Nonetheless, I do get his point — that if we do find life, it’s not likely to have made it much past the basics of cell, membrane, and genetic code. Which got me thinking about something that’s bothered me for a while.

I have been to Mono Lake (pronounced “moe’-noe”), and it is truly an unearthly place. I can see why one might search there for  — as they put it on Wait, Wait Don’t Tell Me this week — yet another alternative lifestyle in California. I know the basics of the chemistry involved, but I don’t know enough to know — as has been claimed by several critics — whether what the scientists have found is highly dubious. According to Carl Zimmer’s roster of experts, it’s all but impossible the authors of this paper performed good science with valid conclusions, although it’s not impossible arsenic-based life exists. (Aside: One of the authors, Felisa Wolfe-Simon, named the bacterial strain GFAJ-1 for “Give Felisa a Job”. Although I normally 100% support such creative naming efforts (scientists are usually dull as dirt when it comes to naming things, and why not name things creatively? One classic example: a development gene named hedgehog inspired the name of a related gene: “sonic hedgehog“), in light of recent events, Felisa’s probably regretting that now.)

But here’s what bothers me about the leap people make whenever they find bacteria that can eat arsenic or live in boiling acid or leap tall buildings in a single bound: that finding extreme life here on Earth makes finding it on other planets more likely. I’m not an astrobiologist, but claims of this sort have always irritated me. They make similar claims because we find life in all sorts of high-wire places on Earth: miles beneath the surface in microscopic rock crevices and pores, in freezing Antarctica, in salt flats, in hot springs, and in barren wastelands of all sorts that support nothing else.

But to me, that misses the point. As far as we know, Earth has, almost from the beginning, hosted a warm, cushy, UV-shielding, stable-chemistry-and-solvent-providing ocean. Almost from the beginning. Granted, the Late Heavy Bombardment could have boiled the oceans away temporarily, but that was a blip. Our atmosphere has gone through at least two great gas revolutions, and the land, initially unprotected by a thick atmosphere or an ozone layer, was a UV-scorched, life-shriveling place. But deep beneath the waves there was always a place of refuge for life to start, to begin, to evolve. In other words, Earth had a cradle where life could begin in relative safety and consistency.

After life evolved in this watery nursery, in which there was no time pressure and plenty of space to work out the basics, gain strength and, one might even say, genetic confidence, it had plenty of additional time — billions of years — to branch out, explore, and master the extreme environments of Earth. Bacteria and archaea may have even been forced into those extreme niches because of competition for the easy life elsewhere.

But what about planets with extreme chemistry or biology that never had a safe ocean; or, had an ocean, but, probably like Mars, had one only fleetingly? Would life have found it easy to begin or have time to take hold in such a forbidding place? Some planets and moons host methane oceans, and Europa may have its own water ocean beneath its icy crust. In those places I might be convinced life could evolve. And there are some life-origin theories that do not require oceans.

But personally, I put my money on the sea. And for the vast majority of places, evidence of extreme microbes on Earth — whether they bathe in acid baths or can get by on arsenic — will not convince me that life in places that have only ever known such conditions is likely*.

What do you think?

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* And I still wish the other bizarro over-the-top microbial life we have on Earth could get half the attention that one little otherwise-relatively-garden-variety bacterium that might be able to survive on a phosphate-free diet gets.

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Review: The Natural History Cocoon http://theartfulamoeba.com/2010/06/06/review-the-natural-history-cocoon/ http://theartfulamoeba.com/2010/06/06/review-the-natural-history-cocoon/#comments Sun, 06 Jun 2010 15:35:42 +0000 http://theartfulamoeba.com/?p=3254

The Cocoon. Creative Commons raindog

Note: Clarification appended

It’s not fair to review an entity one has not experienced oneself. But since the new Darwin Centre of London’s formidable Natural History Museum is in, well, London, and I am demonstrably not, nor easily got there short of a $1000 plane ticket (and I don’t expect the NHM’s going to comp me, especially after this review), I am reduced to reviewing by proxy: through the New York Times review, and my impressions thereof.

If you are not familiar with the newly opened Cocoon at the Darwin Centre, take a mosey on over to the NYT and so so here. Or check out the Darwin Centre’s web site here. In short, the Darwin Centre is the Natural History Museum’s attempt to put the museum and what it does on display in a thoroughly modern way*. Out with Victoriana, in with touch screeniana.

My chief complaint about the Darwin Centre, and its cousins like this exhibit on biodiversity at the Exploratorium in San Francisco, is that they continue the trend of ascepticizing natural history and self-gratifyingly focusing on scientists rather than the real show — the ORGANISMS.

As the New York Times says,

The research facilities and scientists are part of the exhibition; they are glimpsed through windows, framed by explanations. They even become the subject of the show. The Cocoon’s displays are not really about botany and bugs; they are about the collection and study of botany and bugs. The exhibition is really about the museum itself — its methods and materials, its passions and enterprise. I don’t know of another science museum that does this. Along the way, of course, you learn about the natural world, but the real focus is on how that world is studied, and how the museum pursues that goal.

I don’t want to paint the good folk at the NHM in a negative light. I’m sure the designers of this exhibit spent countless hours thinking it through and poring over what way they could best reach the public. They want to teach evolution, the scientific method, and how modern taxonomy works; they want to bring science to life by showing scientists in action. They were given a goal and a budget, and they did their best. I just don’t agree with the goal.

Or rather, that putting this information on display is as important or as interesting and appealing to the public as some other goals. Would you rather go to this exhibit with your child, or one about slime molds or diatoms?  In short, what bothers me most about this exhibit, and the one in San Francisco, is what they seem to say about where biological natural history education is headed. All the effort they put into this exhibit could have been put into making the world’s first Hall of Protists, or Plant Evolution Gallery, or a Bacteria and Archaea Family Album. Instead, we get swipe cards, video guides, sorting games, and generalities — and a rather narrow view of nature. Butterflies, insects, and flowers are great, but what about all the other stuff?

Personally, I find the products much more fascinating than the process. There should be a place to showcase all of them too, and not just the ones with backbones, shells, or exoskeletons. Because learning about the products, while inherently fascinating, almost always leads to questions about the process. After all, Darwin himself started there. He spent five years looking at products while aboard the Beagle.

When I write hear about yeast and their “lifestyles”, or about diatoms, or about pine pollen, or slime molds, or the sex lives of red algae, or about alien pelagic peanut creatures, I’m only scratching the tiniest surface of all the fantastic forms, creatures, structures, and lifestyles that I learned in school. And believe me when I say that *I* only scratched the surface of what’s out there. There is so much more: the fantastically beautiful filaments called slime mold elaters, for example. Hornworts. Nematode-trapping fungi. Where baby ferns come from (not adult ferns). Anglerfish and sea angels. Ping pong tree sponges. Archaea. Radiolarians. Camel spiders. Slime nets. A blizzard of protists and algae and all their mind boggling forms. These things are this blog’s raison d’etre: I want to show and tell you about them not only because I can barely contain my own excitement, but because almost no one else is, at least not in a way the general public can understand.

But I can tell you who should be: natural history museums. A few are trying. I’m particularly fond of the new Sant Ocean Hall at the Smithsonian, which I reviewed here last fall, and which makes an admirable attempt to convey biodiversity through pictures, specimens, and an armada of world-class fossils. I also quite like the evolution and fossils exhibit called “Prehistoric Journey” here in Colorado at the Denver Museum of Nature and Science. My memory is hazy, but I did visit the Hall of Biodiversity at the American Museum of Natural History in New York when it was new about 10 years ago, and I seem to recall it falls somewhere between the two extremes. And, I should note, the Natural History Museum in London itself has just begun what looks to be a fascinating new exhibit (again, I have no plane ticket) on Deep Sea Biodiversity.

I am also a *huge* fan of zoos, aquariums, and botanic gardens because they do such a good job of spotlighting the organisms, but often their signage falls short: it’s vague, confusing, overly technical, overly simplistic, or boring. It doesn’t help you make connections between organisms to understand common structures, interesting adaptations, the general features of a given group, relatedness — or evolution. And lets face it: fungi, protists, bacteria, archaea, microbes, algae, lichens and kin always get the shaft. There is no where you can go to see and learn about them and their forms and variety. But there should be, and as it stands, the natural history museums are the best existing place.

But they too struggle for funding, so it frustrates me that they now seem to be prioritizing and funneling what they do have toward this new once-removed tack toward natural history. Biodiversity and natural history as monolithic concept and scientific endeavor: scattershot, sterile, and boring. Only the choir will find that engaging. The cocoon, at least it seems to me, peering into it from 5,000 miles hence, insulates people from the real stars of the show — messy, wild, weird, surprising, and natural. If we truly hope to convince the world that saving these organisms from climate change and resource depletion is important (and it is, not just for their sake, but for our sake: preserving wildlife keeps the climate stable for agriculture and our water clean for drinking), we should shove the organisms themselves out on stage. All you have to do is take a closer look at them, and with suitably skilled and creative interpreters you’ll find, I think, they sell themselves.

* The Centre was also created to specifically house the botany and entomology collections, not any other groups. I apologize for the omission, but I didn’t realize this was the case until an alert reader pointed it out.

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