The Artful Amoeba A blog about the weird wonderfulness of life on Earth Tue, 11 Mar 2014 16:22:24 +0000 en-US hourly 1 Video of New Hydrothermal Rift Discovered in Galapagos Thu, 18 Aug 2011 14:00:11 +0000

Courtesy of Chris Mah at the Echinoblog, piping hot, fresh video (just weeks old) of a new rift community discovered in the Galapagos by NOAA’s Okeanos Explorer (your tax dollars, should you choose to vote for giving them, at work). One commenter pointed out there’s a red glow at about 1:33 that could even be lava. But mostly, enjoy a few minutes of Zen observing your planet’s fellow passengers, blessedly free of obnoxious Discovery channel voice-over.

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Latest Sci Am Posts and Feedburner Vote Mon, 18 Jul 2011 23:00:16 +0000

Yarrrrr . . . there be a By-the-Wind Sailor. Creative Commons Notafly. Click image for license and link.

Hey kiddos, I’ve been busy over at Sci Am and have two new posts up there, in case you missed them:

The Jellyfish that Conquered Land — and Australia


Circus of the Spineless #63.5

I have a question for y’alls: would you prefer I switch my old feedburner feed over to the Sci Am feed, so that you don’t have to sign up for a new feed (i.e. my old feed and new feed will give the same content from the new site)? Or would you prefer I keep this feed separate, so you can be updated easily on anything I post here? I don’t anticipate posting here super-often, in case that helps.

Again, my new Sci Am blog is at

and the new feed is

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A New Amoeba Era: Moving to Scientific American Tue, 05 Jul 2011 13:20:51 +0000

Mycetozoa, by Haeckel. A beautiful expression of ameoba-hood.

UPDATE: Feed link was previously incorrect. This has been fixed.

Dear Readers,

It has been  a joy blogging with you here over the last two and a quarter years. But someone made me an offer I couldn’t refuse and I have some fantastic news: my blog has been recruited by the new Scientific American blog network, which just launched this morning. Like all creatures, this blog is evolving.

You can find my new blog here and my intro post here, with many more details on my new digs. My new RSS feed will be

I am not sure if I’ll be able to simply transfer my old RSS feed over to this new one or not, but I’ll keep you updated on this if I find it is so.

Bora Zivkovic, our editor, has written a long post summarizing all the blogs (including mine) on the network (and there are about two dozen individual blogs and about 10 more editorial and group blogs) over at

The official press release is at:

Mariette DiChristina’s (Editor-in-Chief) welcome post is on the @ScientificAmerican blog at:

I am very excited about this new opportunity and about the fantastic people I’ll be working with over there. My first (and only the first) blog post will be on a schedule and won’t take place for well over a week, so don’t lose heart when you don’t hear from me for a while. I haven’t forgotten about you guys, and I’ll still be doing what I’ve been doing for two years — only in a slightly different place.

I’ll be keeping this website as well, so check back in occasionally for new posts that don’t fit well at Sci Am or that may get reposted here in order to show off art. This is my professional site and home of my portfolio, and it will continue to be so. So head on over to Scientific American, and check out my intro post, feel free to leave a comment there to say hi, and have a look around at the other wonderful bloggers we have lined up. See you soon.


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The Incredible Inedible Pine Cone Thu, 30 Jun 2011 14:46:15 +0000 This weekend I went hiking in the mountains west of South Park, Colorado. In real life, South Park is a giant, high-elevation plain full of cattle surrounded by legions of snow-capped mountains — NOT a mountain town full of witty, potty-mouthed kids and their clueless parents (although Fairplay, CO, within South Park is indeed home to “South Park High School”). In Colorado-ese, a “park” is simply a high-altitude meadow or treeless plain. There is also a Middle Park — home to the ski resort confusingly named Winter Park — and a North Park, which touches the border with Wyoming and is home to Walden, the “moose-viewing capital of Colorado”.

The biggest treat of a 15-or-so mile hike I did was getting to hike through a real, honest-to-goodness bristlecone pine forest. It was my first time. These can power through 3- to 5,000 years on stony crags in California and Nevada, making them the oldest single living organisms on Earth. Their entire bodies possess this unearthly Sophia-Loren-like aging prowess; unlike most pines, whose needles last two to four years before they’re shed, bristlecone pine needles may hang around for 45.

I had never seen one up close before, and here was a whole forest of them. Dark olive green and indeed quite bristly, they seemed like stiff, bony, but still somehow elegant codgers of the pine world. I snatched a fallen cone in passing. I examined its scales. And sure enough — bristles.

How the bristlecone pine earned its name. As you can see, the bristles shrink as the cone ages. Not my photo -- I was too busy slogging uphill. Creative Commons mcsboulder. Click for link.

In spite of all this awesomeness in just one of their number, plants get no respect. And conifers . . . well, conifers get made into toilet paper (in fairness, so do some deciduous trees). But cone-bearing trees — gymnosperms to botany nerds — are way cool. From their strappy or needle-like laugh-at-dehydration leaves to their incredibly beautiful bordered pit-pocked water-transporting wood cells called tracheids, to their stranglehold of Earth’s real estate from 50-70 degrees North, conifers deserve respect. But for today, let’s focus on their cones. They’re not all bristly, but there’s more to conifer cones than meets the eye.

Gymnosperms are so called because they make “naked seeds”. Not spores like mosses or ferns, nor seeds embedded in fruit like flowering plants. Just seeds — which are themselves plant embryos packaged with a little nutrition to get them going when they land in a spot with promise. Growing up, I was mystified by pine cones because I could never find the seeds. Was the cone the seed? Did the seeds even exist? As it turns out, the seeds are missing by the time you examine a cone because they have usually taken wing on the little sails they sprout. Each pine cone makes two seeds per cone scale, and sometimes you can see the outline of where the pair once sat if you look at a cone carefully.

Here you can see the lighter shadows of where the two seeds once nestled, with a dark stripe between them.

No one home. Creative Commons Analog Weapon. Click image for link.

And here are what winged pine seeds look like. The oil-rich pine nuts you may have eaten are also pine seeds — packed with much more food and lacking obvious wings. Instead, birds called nutcrackers do the dispersal job, stuffing their seed pouches silly (they can cram a hundred or more in there) and burying them hither and yon. Like squirrels, they inevitably forget where they stashed some, which germinate where they’ve conveniently been planted.

Creative Commons keaw_yead_3. Click for link.

Cones actually come in two different flavors, too. The cones I’ve just shown are all females. But there are male cones as well. These are the ones that shed pollen by the lungful and explode in a cloud of yellow dust when you whack a pine branch in spring. (I wrote about pine pollen here).

Male cones are not so heavily armed and fortified as female cones. In fact, you’ve probably seen them before without knowing what you were looking at. They drop in hordes from the tree in spring, once all their pollen has exceeded its use-by date.

Creative Commons gshepherd_br. Click for link.

The male cones shed pollen — really immature haploid plants called microgametophytes, but that’s another fascinating story — that lands in the cones. There, in a truly byzantine process, it takes another 15 months just for the sperm now sealed inside the cone to eventually burrow in through a germ tube from the pollen grain to reach the eggs, and a full two years before the cones open to release their seeds. The pines hold their cards close.

You’ll notice that male and female appear quite different. The females have the bauplan of a well-armored samurai, while the male cones are so wimpy and evanescent that many people are oblivious to their existence. As it turns out, this wasn’t always the case.

A report published online in February in the Proceedings of the Royal Academy B found that, looking as far back as evolution of pines in the Pennsylvanian era some 300 million years ago, female cones were no huskier than males. But in the Jurassic, some 100-150 million years later, they’ve slowly grew stouter and more tamper-proof while seeds and male cones have remained the same size. For a gorgeous photo of a slender fossil female cone next to modern males and females, see here (click the image to enlarge it).

Over a hundred million years of stasis followed by a sudden increase begs the question: why? Well, when things get ouchier and more prone to causing indigestion, one can generally infer that something something started eating them with abandon. That something could have been newly evolved long-necked dinosaurs like Diplodocus. Or it could have been branch-bombing early birds or mammals, or a fiendish new mastication tactic on the part of insects. In any case, once the arms race began, it appears female cones have seen no reason not to continue fortifying, steadily increasing in size to this day. With over two years from pollination to seed deployment in which to defend the young’uns, can you blame them?

In other pine cone news, a paper in PNAS reported in December that those flimsy male gymnosperm cones may well be the ancestors of every flower you see. They looked at which genes are switched on in flower development and compared this to the genes switched on in male and female cone development. In flowers we consider to have retained the forms of the first to evolve — like water lilies — there is often a gradation between petals and stamens(the things that release the pollen), with some petals doing double duty as boy bits (see also here).

Creative Commons Fungus Guy. Click image for link.

They are arranged spirally, just like the arrangement of the “microsporophylls”, or things holding the pollen sacs on the male cone (go back and look). The researchers found that the same genes that govern male cone formation seem to be guiding the development of floral perianths (the petals+stamens) in these early flowers. Further, the genes controlling the development of the tepals and stamens seem to cover a large spatial area and gradually intergrade with each other, just as in male cones. The development of the flowery female bits (the carpels), on the other hand, seem to be governed by the same genes that shepherd female cones to maturity.

Unlike more derived (evolved) flowers like, say, orchids, or poppies, where there are very specific genetic programs for very discrete organs (stamens and petals in these flowers are nothing alike), in these early flowers, it seems as though sepal (another sort of flower part that often encloses the petals), petal, and stamen are still being “sorted out”, in the words of one of the authors. Clearly distinct floral organs goverened by clearly distinct genetic programs evolved later.

So it appears that somehow, somewhere, a male gymnosperm cone got a bit confused and some genes were flipped on that were supposed to be flipped off. Female parts formed amidst the male. And once that happened, some of the male cone scales began mutating in ways that changed their size, shape, and function. Through natural selection, some bigger, showier male scales became sterile as they specialized in attracting pollinators — a new concept, that. With carpel-seeking insects to do your reproductive bidding (rather than just relying on the deveil-may-care wind, as living gymnosperms do), one may presume reproductive efficiency shot up.  Not long after, we have Darwin’s Abominable Mystery: the sudden hegemony of flowering plants, which went on to take over the world*. Today, 90% of land-based plant life makes flowers.

But some of them could still almost make cones. “Primitive” flowers like water lily or avocado still carry around all the genetic equipment they’d need to turn a pine cone — eventually — into a petunia.


*Canada and Russia excepted. It seems flowering trees are no exception to the rule: never get involved in a land war in Asia.

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Fungi in Motion Tue, 21 Jun 2011 14:46:37 +0000 Here’s your Tuesday moment of zen, courtesy of César Sánchez’s Twisted Bacteria blog:

Captured in this time-lapse video taken by one Nick Lariontsev (see here for pictures of the camera setup) is a sampler of fungal growth. In a few cases, it begins with single spores, which would require higher magnification to see. Then, individual fungal threads, or hyphae, sprout and branch in all directions, crossing and recrossing each other. Finally, the group of hyphae becomes a full-fledged mycelium (my-SEAL-ee-um), and then inflates or pinches off certain tips to make spores and sporangia, or spore houses. When the mold changes color from a distance, it is because it is producing colored spores with sunscreen.

You should think of these white fuzzy masses not in sterile petri plates, but in nature. When you turn over a log and see a white mat underneath, you are seeing these filaments. When a fungus attacks a tree, the filaments infiltrate the tree’s cells with a prickly, probing fingers. And when a fungus partners with a tree as a mycorhiza, its hyphae (high-fee) wrap around or penetrate the root — all the way through cell walls to the cell membranes, where they stop so as not to harm the tree. And of course, when takeout spends a bit too long at the Frigidaire spa, it too feels the caress of fungi.

Finally, you see fungus mites briefly at about 3:22, and then again at the very end, where they’re mowing down mold like cows that got into the corn field. In the comments at César’s post, Psi Wavefunction comments that in order to terrorize a mycologist, all one has to do is point and shout “fungus mite!”. I don’t recall every having troubles with them when I was in school, but I can easily believe it. I’ve had enough trouble with aphids and powdery mildews on my plants . . .

Mites are arachnids like spiders and ticks. In fact, mites are in the same taxon (Acari) as ticks. Here’s a close-up of the fungus mites featured in our film:

Courtesy U.S. Department of Agriculture

As for the molds, I don’t know which mold species are which, exactly, except that the tiny black pinheads are probably Mucor, and the grey stuff is likely Botrytis. But for what it’s worth, here are close-ups of conidiophores and conidia (asexual spore houses and spores) of the fungi the author names in the notes as the subjects of the film. All of these molds are extremely common in the environment. Odds are you are breathing in a few of their spores at this very moment. And it’s not cause for panic. Mold spores are everywhere.

Aspergillus fumigatus

Courtesty CDC

Botrytis sp. — so named for the grape-like clusters of spores, and also called “grey mold” for its outward appearance. Ironically, it is also used to produce extremely sweet dessert wines referred to as “Botrytized”. The Germans call it “Trockenbeerenauslese”. Of course.

Creative Commons ninjatacoshell. Click for link.

Mucor — the only zygomycete here. Conidia are housed in a sporangium that looks like a Q-tip (sorry — “cotton swab”).

US Department of Agriculture, Agricultural Research Service, Systematic Botany and Mycology Laboratory

Trichoderma. Conidia (asexual spores) are at tips of “phialades”. They blow them up like balloons. In the photo below you can see them in various stages of inflation.

Courtesy U.S. Department of Agriculture


Creative Commons keisotyo. Click for link.

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When Cells Discovered Architecture Mon, 13 Jun 2011 17:05:32 +0000

I have a new guest post up today over at the Scientific American Guest Blog on a newly discovered cache of the earliest known big multicellular life — and how some of it (but definitely not all) is startlingly like stuff alive today, 600 million years later. Go check it out!

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Lichens in the Mist Fri, 10 Jun 2011 17:44:47 +0000 A few weeks ago I was graciously allowed to accompany local lichen expert Ann Henson on one of her field trips. It was a cold, cloudy, and rainy day at about 8000 feet in Colorado’s Front Range, and by the end I was chilled through. I didn’t care. I learned loads from Ann and took lots of photos. Today, I bring you a fun slideshow of a few of the things we discovered on the trip.

First, a refresher. Lichens are fungus/algal collectives in which it may be a partnership or may be something more sinister on the part of the fungus. The algae are trapped in tangles of fungal filaments and sandwiched between two protective cortices (sing. cortex). To whit:

A and D are the upper and lower cortices. B is the algal layer. C is the medulla. And E are the root-like structures called rhizines. For you botanists out there, this should remind you of something — the cross section of a leaf. Convergent evolution in action again, my friends.

The algae photosynthesize and make the food. The fungus provides a place to live that protects the algae from death by dryness and sometimes provides sunscreen. Though “lichen usually” means one fungus and one alga (conservatives would be happy), it sometimes means one fungus and a few algae (not so happy). The following is one such case.

Here we have the common freckle pelt, Peltigera apthosa. These things can range from bright green when they’re wet to greyish brown when dry and sad. In most of the lichen, the green eukaryotic (nucleated) algae Coccomyxa

Photo by Oregon State University

holds sway, but the second spouse photosymbiont Nostoc

Creative Commons Kristian Peters

gets its own little house (the freckles on the freckle pelt in the photo above, also called cephalodia) because apparently partner 1 and partner 2 don’t play nicely together. Notice the bigger cells in the chains of the cyanobacterium Nostoc. Those are called heterocysts and those particular cells can do something most living things cannot: fix nitrogen. Something like 70% of the air you breathe is nitrogen (N2) but turning it into a form living things can use (like NH4, ammonia) is difficult.

Thus nitrogen is a limiting nutrient in most biological systems, and creatures that can make it get extra street cred and often special cushy living arrangements. The nitrogen-fixing bacteria that live with legumes are one such case (thus the invention of crop rotation to keep fields fertile), and so can Nostoc. Hence the quirky living arrangements in Peltigera. If someone made a TV show about this thing, it would have to be called “Big Lichen”. When reached for comment, Coccomyxa admitted the relationship was strange but said it was sometimes fun to sneak out for algae-nights-out with Nostoc and that having more than one alga in the relationship really helped relieve the pressure to put out glucose. But I digress.

The reddish-brown curvy things on the common freckle pelt are the apothecia, or disc-like reproductive strucutres of the fungus. This is where the fungus half of the lichen gets busy, making its ascopores (sexual spores) in sac-like structures called asci (ass-eye). Here’s a cross section of one in an un-lichenized cup fungus:

So these little cups, or apothecia, are a visible demonstration that a fungus is part of the lichen mix.

Here’s our next subject:

This is Leprocaulon — the “cottonthread lichens” – either Leprocaulon gracilescens or Leprocaulon subalbicans, probably the former. I had never seen this lichen before in my life and it was an odd one. Ann described it as being “barely lichenized”, and it is a collecting of threadlike granular fibers that stand up from the surface they’re growing on by a centimeter or so. It’s soft. Really soft. The upright fibers move back and forth easily, and when I gave it a pet it was not unlike touching dryer lint. Not like the typical crusty, papery, or fibery lichen at all.

The next two lichens got me really excited.

These dark patches are jelly lichens, and they are what happens when Nostoc rules the roost. I’m not sure of the genus, but it may be Collema or Leptogium. Their fungi are monogamously lichenized to cyanobacteria, and this gelatinous, brown mass is the result. True to their name, they were rubbery and fun to squish gently between the fingers. Interestingly, when Nostoc makes giant colonies of itself on its own, it doesn’t look much different.

Creative Commons Lairich Rig

So I guess we know who’s wearing the pants in this relationship.

Next we have what Ann called the most spectacular lichen in Colorado, and I agree. To give you a sense of scale, I could easily sit on the rock in the center of this photo.

This is rock tripe, also called Umbilicaria americana. It is unique to our hemisphere. Generally speaking, when the rock looks like its gotten a really bad sunburn and is sloughing its skin, that’s rock tripe. I think it’s called tripe because it was what one could eat when there was nothing better left. True to its generic name, it is an umbilicate lichen. You had an umbilicus once too; it attached you to your mother. Umbilicaria keeps its umbilicus thorughout life. It attaches it to its substrate — in this case, a rock. Look carefully at the photo below. This Umbilicaria is about three or four inches across, or more than 15 cm. The white raised portion overlies the umbilicus underneath.

You probably wouldn’t guess it from looking, but the underside is pitch black and fuzzy.

And, of course, something has found a way to rain on even Umbilicaria‘s parade.

It’s another lichen growing on top of it. This reminds me of one of my favorite lines from Jurassic Park: “Life finds a way.” (although obviously, not always, or we wouldn’t be facing an extinction crisis of staggering proportions that makes me feel both blindingly angry and supremely helpless).

Speaking of de-motivational events, on our way out, we saw this:

Yes, those are two giant sets of bear claw scratch marks on that tree. Though bears aren’t known to eat lichens, I believe they are known to eat hikers. Time to go find some hot chocolate . . .

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3QD Voting is Open Sat, 04 Jun 2011 17:05:45 +0000 UPDATE2: That’s Friday at midnight! Please go have a look and vote ’em if ya got ’em!

If you’d like to vote in the 3 Quarks Daily Science Blogging Contest, go here. I have two posts in the running, but I particularly like is this one. Voting closes on June 810. Thanks to any of you who vote!

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All Mushrooms Bright and Submersible Mon, 30 May 2011 23:59:32 +0000 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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Must Enter to Win Fri, 27 May 2011 16:04:30 +0000 UPDATE: Voting is open now here. Please consider voting for my bombardier beetles post!

As usual, Three Quarks Daily is having their annual science blogging contest, judged this year by physics babe (and yes, I know I’m perpetuating stereotypes here) Lisa Randall. I’m not very good at self-promotion. But as Ed Yong recently admonished, it’s important to enter science writing contests, and this one happens to require a little self promotion.

You can nominate one and only one blog post in the contest, and if you choose to do so, it must be a post written between May 22, 2010 and midnight on May 31, 2011 (the deadline for entries). If you choose to nominate me, you can select anything you like, but here are a few of my favorites. This is also a great opportunity to catch some of my favorite posts that you might have missed over the last year:

One nomination for one post is sufficient, so if you see in the comments at 3QD your favorite post already entered, it’s taken care of for now. You can nominate another post (by me or anyone else) instead if you wish. But having too many posts nominated might split the vote, so if you don’t feel so moved, please don’t feel you need to nominate. Once the nominations are in, there will be a voting stage to cull the top 20 entries.  I’ll let you know when that happens, should you like to vote for me. Danke schoen!


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