So what’s actually going on in the mitochondrial video? Well, I’m not sure of every detail, but as a former biochemistry TA, I can give you a lot of educated guesses. The movie appears to begin with mitochondria — sub-cellcular power stations — inching along a part of the cellular skeleton called microtubules. The job of mitochondria is to finish the process of turning the energy stored in the bonds of glucose into useable power through respiration. As energy is harvested from the electrons prised off glucose, they are finally passed to oxgen, which accepts them along with some hydrogen ions to form water. Meanwhile, the carbon that was tied up in glucose ends up as carbon dioxide. This forms the basis of your inhalation of oxygen and exhalation of carbon dioxide with each breath you take. Anyway, back to our film.

Then an (?)amino acid chain (fragment of a protein) of some sort escorted by (?)chaperone proteins enters a mitochondrion via a pore through its double membranes*. Then you see the contents of the mitochondrion: an asteroid field of colorful proteins zipping about amid strands of the mitochondrion’s DNA.

Then, looming in the distance like the Pillars of Hercules (or the warship encrusted columns inside the motherships in Independence Day — which seems to be the point. They are going for cinematic here.) are tubular mitochondrial cristae, or folds of the inner membrane. These folds increase the surface area available for respiration.

Embedded in these columns are the rotary engines of mitochondria — enzymes called ATP synthases. These proteins are fascinating feats of natural selection that rotate as they charge their substrates (the molecules they will act upon): namely, ADP. Swarming around these proteins like fireflies are hydrogen ions (H⁺ — essentially, a proton, but often surrounded by three oxygens in aqueous solutions) generated by stripping glucose of electrons like a car in chop shop.

Without going too deep into the gory details, when a cell burns glucose, it performs some preliminary reactions in the cytoplasm (glycolysis) and sends the remaining energy-bearing bits into the mitochondrion for full processing. After enzymes performing the Citric Acid cycle in the interior of the mitochondrion (called the matrix) squeeze more power out and release what’s left of the glucose as carbon dioxide (CO2), the electrons glucose has yielded are passed down the electron transport chain of proteins embedded in the inner membrane, which use the energy thus released to pump hydrogen ions out of the matrix into the space between the mitochondrion’s two membranes. I think you can see this happening at about 1:08.

The inner membrane, unlike the outer, is highly impermeable to most molecules — even to tiny hydrogen ions. The resulting ionic gradient can only flow back downhill through a rotating pore in ATP synthases**.  The passing hydrogen ions powers their rotation and their charging of ADP to ATP, the cell’s energy currency (an explanation of this fascinating mechanical process can be found here under “binding change mechanism”). It’s such a clever system that engineers have designed engines (called the Wankel Engine) based on the same principle and built them into working cars — namely, the Mazda RX-7 and RX-8. I know this because one of my biochemistry professors at Cornell had actually owned one of these for that very reason (You know you are a nerd when . . . ).You can see the biological version of this process happening at about 1:15, where small molecules enter the head of the synthase, light up to let you know they’ve been charged, and then are released to please go play nicely with the rest of the cell.

Here is a conventional representation of what I just described — I, II, III, and IV are proteins of the electron transport chain, NADH is an electron ferry that shuttles said particles from ex-glucose pieces to the electron transport chain, and succinate is an intermediary in the citric acid cycle (for those that remember, this is the step that generates FADH2):

During all this action in the movie, the camera also passes once or twice through the undulating lipid bilayer of membranes, where the kinky double-tailed (and faintely spermish) phospholipids jostle against each other to keep the membrane fluid. Mitochondrial membranes actually contain many fewer sterols (cholesterol is one — they are molecules that help stabilize membranes) than the cell membrane, giving the mitochondrion greater shape-shifting powers.

I think the next-to-last scene is an ATP/ADP transport protein that actively shuttles ADP into the matrix and ATP out. Finally, you see all the mitochondria swarming toward some big shiny thing (centrosome? endoplasmic reticulum? Who knows! Scene list please, Harvard!) like star cruisers converging on a galactic rendezvous. Actually, mitochondria do sometimes cluster near where they are most needed. For example, in cells with flagella, they may cluster near the base of the tail.

All in all, the mitochondrion’s a tightly run ship. Lest the ID community use these incredible little machines as evidence of “stasis” or “irreducible complexity”, let it be known that anaerobic (non-oxygen breathing and non-mitochondrial) bacteria alive today have proteins almost identical to ATP synthase that function in reverse: powered by ATP, they serve to detox the bacteria of H⁺ to rid them of the acidic by-products of the less-efficient but still-better-than-nothing energy-producing process of fermentation. The cytochrome complexes (aka I, II, III, and IV, the cogs of the electron transport chain) may have evolved for similar detox purposes in other ancient bacteria before being combined with ancient ATP synthase by natural selection to form the well-greased respiratory engines we have today.

Typical plant and animal cells contain hundreds or thousands of such mitochondria, though their number ranges from one bizarro giant in a few single-celled protists to several hundred thousand in well-provisioned egg cells. I’m not certain why the directors of this film chose to show this mitochondrion with tubular cristae. Most vertebrates have regular laminar, or sheetlike, cristae (remember that it was unusual that alvaeolates (the paramecia, ciliates, dinoflagellates, and apicomplexans) had tubular cristae), though plants have both sheets and tubes in their mitochondria, and are more irregularly shaped and sized.

Of course, proteins inside mitochondria don’t really float around looking like someone blew up a box of Trix in the space station. In reality, my understanding is they’re all sort of, well, clearish at that scale. And in this thorough NYT article on recent advances in molecular animation, scientists acknowledge that molecular animators also take liberties with space.

“Some animations are clearly more Hollywood than useful display,” says Peter Walter, a Howard Hughes Medical Institute investigator at the University of California, San Francisco. “It can become hard to distinguish between what is data and what is fantasy.”

But clearish molecules and vast distances would make for a pretty dull movie, so I don’t begrudge them their colors. This situation reminds me of the Peter Jackson Conundrum: was the Lord of the Rings better before your head was filled with Peter Jackson’s version of everything? And wasn’t it better when only the people who actually took the trouble to do all the reading were in on the magic?

My gut feeling is that these movies are a good thing, as is sharing the wonder with the masses. If we wish to make the case to society that science is important and worthy of time and money even on its own terms, animations like these help. It is also unquestionably cool to see it all in such detail — revealing things we could not easily foresee without seeing everything together in glorious living color — even if our imaginations are a bit impoverished for it. It’s a worthy sacrifice, in my opinion, if our appetites are whetted.

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* The outer membrane is a product of a long-ago engulfment of a bacteria by a predatory cell — the inner membrane is the ancient bacterial membrane and the outer membrane is the erstwhile vacuole. Further evidence for endosymbiosis includes that mitochondria (and chloroplasts) have their own single, circular (like most bacteria) DNA-based chromosome without a nuclear membrane from which they manufacture their own proteins and bacterial-sized ribosomes (which can even be interchanged with bacterial ribosomes in some cases) and replicate by division. They’re bacterially-sized too: 1.5 by 2-8 micrometers.

** In high-magnification photos of mitochondria, you can actually see the ATP synthases poking into the matrix like lollipops.

I’m torn here. On the one hand, this is really cool. On the other, it somehow feels horribly wrong. I mean I’m sure it’s not much more wrong than what I do to baker’s yeast every time I bake bread. But . . . I don’t toy with the yeast before I incinerate them. Yeesh.

Anywho, for those who are unfamiliar, paramecia are classic organisms used to teach high school and college students about microbes. But they’re not simply boring microbial lab rats. They’re fascinatingly formed, filled, and operated little creatures. They are often described as “slipper-shaped”, or, as van Leeuwenhoek would have it, “slipper animalcules”. In this video, watch for the little cilia beating all over the cell’s pellicle, or membrane+submembrane shell.

So let’s have a tribute to the humble Paramecium today — we’ll take a closer look at a microbe you might think you already know. Think again. Take a look at the basic paramecium formula here (I can’t post it because I don’t have copyright). I’ll refer to the various parts of this diagram as we go along.

Paramecia are ciliates, protists coated in little beating hairs called cilia for at least part of their life cycle. In photographs where only their cilia are stained or photographed with scanning electron microscopy, paramecia look like ovoid shag rugs (or see here or here). These cilia can beat in forward or reverse with extreme precision — much more precise than large flagellae or lumbering pseudopods. When beating in foward or reverse, the paramecium moves in a spiral motion around an invisible axis — and they can throw it into reverse in a ciliumbeat to avoid obstacles or “negative stimuli” (cough).

Inside the cell is a contractile vacuole used to bail out water against the perpetual osmotic gradient (the inside of the cell has a higher solute concentration than its watery surroundings, leading water to constantly seep through the membrane by osmosis, like a leaky ship), various vacuoles (spherical storage vessels) for digesting food and excreting waste, and at least one micronucleus and macronucleus.

The micronucleus, of which there may be as few as one or as many as 80, is diploid, or contains two copies of all the DNA, just like all of your cells. But the macronucleus may contain 50-500 times as much DNA as the micronucleus (the Paramecium aurelia macronucleus is 860-ploid, according to one of my biology texts). The micronucleus is all about passing DNA to mating partners for sexual reproduction (aka swapping genes), while the macronucleus is in the business of pumping out messenger RNA and getting it translated into proteins.If you remove the micronucleus, the cell can divide asexually another 350 or so times before dying of no sex (yes, in ciliates, this can apparently happen). But if you remove the macronucleus, the cell immediately dies.

On the surface of the cell is a funnel-shaped oral groove that guides food particles toward a pocket where food vacuoles are created. Enzymes get pumped inside to digest whatever hapless bacteria, yeast or “other” finds its way inside. Many paramecia may contain symbiotic bacteria living within them or even within their macronucleus, perhaps providing vitamins or other growth factors that would otherwise be hard to get. One paramecium even has photosynthetic symbionts. Paramecium bursaria, which has ingested and partnered with the green alga Zoochlorella.

These are *not* chloroplasts, or rather, they are not homologous to (share a common ancestry with) the chloroplasts in plants. Plant chloroplasts are ingested cyanobacteria. Zoochlorella are chloroplasts in the sense that they are internal photosynthetic symbionts, but they were free-living eukaryotic (nucleated — not bacterial) algae before ingestion. But here’s the mind-twister: the chloroplasts within the Zoochlorella are homologous to plant chloroplasts, because plants evolved from green algae.
This is the only Paramecium known to do this. To what extent the Zoochlorella could pop out of that paramecium and get along on its own or is degenerate and helpless I do not know.

Paramecium bursaria, a rare symbiotic photosynthetic paramecium. Love the gorgeous detail. Creative Commons PROYECTO AGUA**/**WATER PROJECT

Some large ciliates may hold the land-speed record for all protists. They can cruise at a blinding 2 millimeters per second, which, assuming a 250-micrometer paramecium and a 5.5-foot human [calculator tapping noises], is the equivalent our 5.5-foot human swimming  a blazing 30 miles per hour*. And they are backstroking at these speeds through a medium that has the viscosity (to a proist) of molasses.(See the middle of Psi Wavefunction’s post here, or for the physics-buff bionerds out there, the original 1977 paper “Life at [a] Low Reynolds Number” here).

Paramecia are also armored with a built-in defense system. Their pellicle is laced with dart-tipped harpoon-esque “trichocysts” (a specific type of a more general organelle called an “extrusome“, which is clearly another case of convergence (independent invention of the same structure) with jellyfish nematocsyts), which deploy explosively within milliseconds if the paramecium feels threatened, is feeling peckish, or perhaps needs a convenient anchor while it tucks in to dinner. See how they look retracted here, and how they look once fully-expelled here, which this site describes as the “disheveled porcupine” look. The bottom photo is of undeployed trichocysts in the pellicle**.

Known diversity in ciliates, ca. 1904, by the incomparable Haeckel

Paramecia are, as mentioned, ciliates. There are something like 9,000 species in fresh and salt water, and their complexity and diversity of form is astounding. Some of the most complex species come close to replicating the digestive systems, muscles, exoskeletal systems and even vertebrae so characteristic of multicellular life within a single cell. According to one of my biology texts, ciliates have produced the greatest specialization of subcellular organelles of any protist. Rest assured you will read more about the creatures in this group at this blog.

Ciliates fit into the larger taxon (group) called alveolates, a term you may recognize from high school biology as the name for the little sacs at the ends of the passages of your lungs. The structures are similar; the Latin just means “little cavities”, and in ciliates like Paramecium they are little membranous sacs found just below the cell surface engulfing the roots of cilia. Though the ciliates like Paramecium and the dinoflagellates and parasitic apicomplexans may seem worlds apart, they all share this feature and several others*** that reveal their common ancestry. See how the ciliates fit into the alveolates, and how the alvaeolates fit into the eukaryotes here and here.

Before I leave you today (or is it the other way around?), enjoy this video of some more active paramecia tooling around with a bunch of nerdy Euglena (the little guys). Because before you allow your little microbial minions to be devoured by Pac-Mecium or taunt them with a chemical blast, remember: were they your size (or you theirs), you’d never survive the hairpin extrusome assault mechanism, and they’d be gone before you knew what hit you. : )

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*or 48 km/hr for you metric users. According to the intertubes, the fastest human swimmers can go is around 5 miles/hr over very short distances. Of course, their bodies are not covered in highly-efficient propulsive cilia (and more’s the pity).

**With all this weaponry, forget Pac-mecium. Helloooooo Ultimate Paramecium Fighting League.

***including, for the bionerds out there, tubular mitochondrial christae, “closed mitosis” in which the micronuclear membrane doesn’t dissolve during mitosis and the mitotic spindle forms inside it, and similar “extrusive organs” like trichocysts

Video is, unfortunately, in German. If you don’t speak German, consider making up your own (PG) translations to key scenes and sharing them with us in the comments! : )

In the beginning you see the free-living amoebae (I think) happily wandering about on their own with some fungal filaments (called hyphae, high’-fee) growing at the top of the screen. Then the ameobae start aggregating — crowding after each other like sports fans filling a stadium. The species uses a famous signaling molecule called cyclic AMP (cAMP) to coordinate their union, and it passes through the swarms in pulsing, spiraling waves noticeable at about 1:35. If I’m using my extremely poor knowledge of German correctly, the narrator is nothing that hundreds of thousands of amoebae join together in the process. They do not fuse membranes; they retain their cellular identity.

Notice that some amoebae get left behind or lost in the process. At 2:47 you can actually see some break out of line and go back to being  little amoebae at the very tail end. After the spiraling and pulsating business is done, the mass stretches into a slug and crawls off. At some point between forming the slug (also called a grex) and making the sporangium (the house where spores are made), the amoebae get it on and mix some genes.

When the slug decides conditions are perfect, it stops, puddles up, and then stretches skyward. The lucky amoebae who will become spores riding up the stalk like an elevator. Those stalk cells get the rotten end of the deal — they must sacrifice themselves to ensure their comrades can reproduce. This little detail has led scientists to study these organisms in order to better understand altruism and cheating in nature. What they’ve found is that, as ever, things are not always as they seem. Some would-be stalk cells indeed give their lives, but others buck the system by cheating. Yet if everyone did, the system would break down entirely. There are, as you may imagine, some very interesting dynamics and mathematics governing this system.

Finally, a roving madsnail goes on a rampage wantonly destroying the beautiful slime mold gardens. Stupid animals.

Incidentally, D. discoideum is the species I wrote about in January in which some strains were recently discovered to practice agriculture, or something close to it, by taking bacteria of their preferred noshing type with them in their spores so they have a guaranteed food source when they land. And still more recently, scientists published an article in Science (see here and here) they may even have tissues — and use two signaling or regulatory proteins related to the ones animals use to organize their embryos during development. This seems to mean the common ancestor of slime molds and animals (whatever *that* might have looked like) was using ancient versions of these proteins to arrange itself, and its descendants — both slime molds, and you — inherited these same proteins and are still using them to organize their bodies, in their different ways.

Cellular slime molds represent one of life’s many experiments in multicellularity. You are the product of another. So are plants. And so are fungi, and brown and red algae and some blue-green algae — and there are many more. Other experiments seem to have been abortive; recently this article revealed that blue-green bacteria (aka cyanobacteria) dabbled in multicellularity many times. Remember: evolution isn’t a goal-directed endeavor, although in certain etremely successful groups (vertebrates, beetles) it may seem that way.

To see a different cellular slime mold species that makes violet sporangia on slime mold candelabra, see here. Spectacular.

Finally, I’d like to note I have a new favorite German word : Schelim. As in “schleim mold”. : )

HT to this post at Small Things Considered for the discovery of this wonderful and educational German film.

You are witnessing one of nature's most incredible migrations that never gets shown on the Discovery Channel. Believe it or not, each one of those little dots is a solitary amoeba. But not for long.

Note: This post contains a prize inside! It will await those patient enough to dig to the bottom. : )

Regular readers of this blog know well about my weakness for the protists formerly known as slime molds (scientists know apparently prefer the more PC and sexy “social amoebae”, although how you can get much sexier than “slime mold” I really don’t know). Exciting news came this past week that a species of cellular slime mold — Dictyostelium discoideum — contains members who have taken up bacterial farming (or at least husbandry — more on that distinction later). I ask again — slime molds: is there anything they can’t do*?

Before we get into their new status as potential FFA members, let’s talk a little bit about this particular group of slimes. So far on this blog, I’ve told you primarily about a group informally called “plasmodial slime molds”. This is the kind that make big, colorful slimy slicks that rove the forest floor wreaking microbial havoc as they vacuum up any bacteria, yeasts, and protists in their path, and then blossom into beautiful bright fruiting bodies like the one in the masthead of this blog.

But there is another kind of slime mold. One that, while perhaps less glamorous, is even more crafty and incredible: the dictyostelids, or cellular slime molds. What is the difference? Well, if plasmodial slime molds are amoebas that discovered living large, cellular slime molds are amoebas that discovered living social. In a plasmodial slime mold (also called myxomycete or myxogastrid), two amoebae meet, decide to spend the rest of their lives together, fuse, and then that fused cell starts dividing mitotically, or asexually, like it’s going out of style to churn out hundreds or thousands of genetically identical nuclei inside one big happy bag of cytoplasm.

In a cellular slime mold, something even more remarkable happens: a single amoeba called a myxamoeba suddenly decides it is starving. As a result, it secretes a molecule called cAMP as a distress call**. And suddenly, hundreds, thousands, hundreds of thousands of amoebae amplify the call by emitting their own cAMP, and begin streaming in toward Amoeba Zero in pulsating waves. They get sticky, climb on top of each other, and cling together. The pile towers up. And then, if it’s not sufficiently bright enough, the tower topples and begins sliming around like a slug. It’s now a single multicellular organism — made of 10,000 to 125,000 amoebae who still retain their individual membranes and identities. Yes, like the Borg — if they were all crazy-glued together. And if they intermittently all lived happily on their own before feeling an irresistible pull to join something called a “collective”.

Take a look at this process:

That aggregation star at left is a schematic of what you're seeing in the image at the top of this page. Tijmen Stam, IIVQ (SVG conversion) - user:Hideshi (original version) GFDL + CC-BY-SA, click image for link.

After crawling far enough to reach an area deemed suffienctly light (I imagine this it to raise the odds of being in a windy, spore-dispersally spot), the slug coalesces into a sombrero-shaped mass from which some of the cells begin gliding upward along a stalk like an elevator. At the apex, the elevator cells convert themselves to spores. Ultimately, they blow away in the breeze to (hopefully) more bacterial pastures.

Now take a look at this process in action.

• First, here’s an overview from my alma mater — the Plant Pathology department at Cornell (Try the downloadable versions if the player doesn’t automatically load or if you want to watch a high-res version (recommended)). Watch the perimeter and the background. Note slugs wandering about looking lost.

• Now let’s look at it up close — scroll down and press play on video at right. Note straggler amoebae.

And it gets better — or worse, depending on your perspective. Some of the amoebas in the slug must voluntarily sacrifice themselves (a process called programmed cell death, or apoptosis. It’s basically microbe seppuku) to form the long stalk. This seems to be determined primarily by what phase of the cell cycle they were in when they reached the forming slug; the last cells to arrive will form the tail of the slug, and the early-arrivers at the head of the slug will become the sacrificed cells of the stalk.

But in an entity where not all cells are genetically identical, you can see how it might be tempting (and much more reproductively successful) to shirk stalk duty and climb your way to the top come hell or high water — that is, to cheat. And in fact, it turns out cellular slime mold myxamoebae do sometimes cheat their way to reproductive success. Scientists fascinated by this have studied it a lot.

That brings us back to farming. Because in addition to being cheaters, some Dictyostelium also appear to plan ahead in other ways. Like packing lunch — or perhaps the seed of lunch. They bring their preferred bacteria with them and seed the soil where their spores land. It’s a little too early to tell if they just eat what they brought or wait sufficiently long for what they brought to reproduce a bit. But the evidence so far seems pretty conclusive: some D. discoideum spores are packin’ bacteria. Though whether they are packin’ them inside or outside the spore wasn’t entirely clear to me either. Only 1/3 of the samples they tested were farming amoebae, but that may be because it does come with a price. Farming amoebae are fitter in times of starvation, but less competitive than non-farmers in times of plenty. Having both strains around makes sense in a world of changing conditions.

Because they don’t weed, water, or fertilize their future food, some scientists suggest it might be better termed husbandry than farming. Whatever you call it, these are the first microbes ever known to do it. Cool***. And the reason, scientists told National Geographic, is that these are also the only microbes that are social — being social enables wind-blown, stalk-borne dispersal, which makes bringing bacteria worth it at all. And so far as we know, all the planet’s other farmers are all social organisms as well. EEEN-teresting.

From Science magazine’s writeup:

Koos Boomsma, an evolutionary biologist at the University of Copenhagen who did not work on the study, is not surprised that farming is scattered through the tree of life. “But if I would’ve had to predict where I would have next expected farming to be discovered, I would never have predicted a slime mold,” he says.

See, this is exactly what happens when we underestimate slime molds. And you all thought I was kidding about that world domination thing . . .

This discovery got full court press coverage; you can read more about it here, here, here, here, here, and here.

When first discovered, slime molds — both plasmodial and cellular — were thought to be fungi, hence the “mold” bit. But unlike fungi, they have cellulose cell walls (like plants and some other protists, but not chitin, like fungi) and cellular organelles called centrioles (like animals). Moreover, the two groups were not thought to be closely related to each other****. Now we know that although there are other types of slime molds that do not fit into these two groups, the plasmodial and cellular slime molds are true taxonomic groupings reflecting common ancestry, and that the two groups are fairly closely related: they are both in the same taxon as free-living amoebas — the Amoebazoa (look for the group on this tree, and then click on it to explore. Notice on the big tree they’re on the same branch with animals and fungi). Which makes sense — slime molds all begin life as ordinary looking amoebas.

Now bear in mind Dictyostelium, for all its transcendent coolness, is but one species among many — perhaps hundreds or thousands. What are other cellular slime molds like? Well, we may not know what many or most of them are like, since so few people study them. But below are videos (your treat for making it all the way to the end of this post) of a spectacularly beautiful other species of cellular slimes, Polysphondylium violaceum (Paul-ee-sfon-dil’-ee-um vie-o-lace’-ee-um — say that three times fast). Unlike Dictyostelium, it does not make roving slugs (though it does aggregate), and it uses a chemical called glorin, and not cAMP, as its chemoattractant. Watch the complex fruiting bodies — or sporocarps — form in these time-lapse movies again from my old buds in the Plant Path department at Cornell.  Notice in particular the branching and the purple pigment — it’s like a fireworks display in slow motion. Try pausing the videos just before the end for a nice still. And again, try the downloadable versions — they’re much higher quality images anyway.

• Video 1 — close up
• Video 2 — wider angle, different sample, even more spectacular display

Yes. Ameobas can do that.

Finally, ponder this: Dictyostelium, and the cellular slime molds as an entire group — was not discovered until 1935 in a North Carolina forest. 1935. Now ponder all the other amazing stuff that must still be out there, just waiting.

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*Perhaps home decorating.

**cAMP is a ubiquitous Earth signaling protein found in organisms from humans to bacteria. It’s a stripped down ATP ( the energy currency of the cell) used, essentially, as one of several master switches for turning circuits (metabolic pathways) on and off in the bioreaktor/ Brownian chaos computer of the cell (Many, if not most, of the biochemical reactions of the cell are governed merely by the rate at which molecules happen to randomly bump into one another (implication: more molecules will make the reaction go faster). Even proteins chaperoned to important reactions by other proteins must bump into their chaperones in the first place.) In social amoebae, cAMP takes up the somewhat novel role of chemical attractant — that is, a pheromone.

***There are a few more lurid and/or fascinating bits to the cellular slime mold story. For one, lest you think their asexual reproduction was the only weird thing about them, Dictyostelium sex is also kinda creepy. It starts out normally: two amoebae meet and fuse. But things get weird fast: the zygote (diploid, or double-chromosomed) offsprings goes on a cannabilistic rampage, engulfing all nearby amoebae as fast as it can. When sated, the cell wall thickens with cellulose to form the resting spore, or macrocyst, that can survive tough conditions. Before it germinates, the cell undergoes meiosis, or reductive cell division, to get back to one copy of chromosomes per cell, and then several mitotic, or regular, cell divisions before it releases its little myxamoebas when conditions are good.

**** From my late-90s botany book: “The plasmodial slime molds, or myxomycetes, are a group of about 700 species that seems to have no direct relationship to the cellular slime molds, the fungi, or any other group.”

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. : )

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

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

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

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

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

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

An Antony van Leeuwenhoek original: Portrait of the Ash Tree as a Young Cross Section.

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.

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:

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 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.

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!