Field of Science

Moss Microforay

Occasionally, I do go out. In anticipation of such an unlikely event, I usually have an eppie tube or two and possibly a ziplock bag in my pocket. In that case, I collect random samples of whatever I'm in the mood for, and abuse my work-related scope access privileges engage in highly legitimate microscopy practice. I like to take pictures, and although I have a long ways to go to reach the professional protistology levels, I try...anyway... <_< So here was one such foray, where I collected a wet moss sample, and added a drop to a slide. Turned out to be teeming with life:

As for identification, I only have a faint idea for the most obvious ones. The rest stump me clueless. But I'll try. Any real protistologists out there, feel free to help out!

Plate I:
A - Test of some sort of amoeba. Euglyphid?
B-E - green algae of sorts
F-H - ? algae...
I - a young hypha emerging from an fungal spore (awww, so touching!)
J - ???
K - green algal like thing again
L - amoebozoan test?

Plate II:
A-C - green algae, although C may be some sort of photosynthetic excavate for all I know...
D - fungus?
E - generic round biflagellated algal thingie (probably as far as one can get without molecular analysis)
F - a spore?
G-H - amoebozoans
I - too small for a nematode I think... so perhaps a euglenid of some sort?
J - timelapse of some non-photosynthetic motile flagellated thingie
K - Euglyphid!
L - green algae of sorts
M - ??? Algae. Of sorts.

Someday I hope to fail less epically at this kind of thing. Perhaps is some protistologist out there is willing to train me. As a grad student. Or something... /explicit self-advertisement

Sunday Protist -- Xenophyophore

Possibly the world's largest cell:


A deep-dwelling marine foraminiferan (Kingdom Rhizaria) that is one large multinucleate cell. They can grow up to 25cm in diameter!
More information here.

What is a protist?
The Eukaryotic Tree of Life

There seems to be lots of confusion as to what a protist really is. This is quite understandable, since the chaos has deep historical roots.

The definition (guideline) that most protistologists tend to follow is:

Any eukaryote that is not a plant, an animal, or a fungus.

ie., the other ~98% of eukaryote diversity!

Let's take a look at this diversity: (Keeling et al. 2005, Trends Ecol. Evol.) (free access)

Assignment: Find animals and land plants. Note relative significance and diversity!

And before a microbiologist wanders by and launches a massive attack on my eukaryocentric ego, I'll put things into perspective: (Ciccarelli et al. 2006, Science) (free access)

K, now that this is over with, back to ignoring prokaryotes...

Why is Protista such a cladistic mess?

Historical reasons, mainly. Only a couple centuries ago, people still classified life into things that were motile (animals) and sessile (plants). Fungi were plants because they didn't walk. (molecular evidence shows they're actually the sister clade to animals). Microscopic life was unknown at that point, so there was very little reason to suspect any of those strange organisms even existed. And seaweeds were plants as far as anyone was concerned. Not like it's actually obvious without examining the cell structure and molecular data.

Eventually, this system failed, and attempts at patching it up eventually led us to a tangle of taxonomic chaos. Thankfully, molecular biology has allowed the eukaryotic phylogeny to be resolved quite a bit better (but still with plenty of vagueness).

Another problem is convergent evolution screwing up morphology-based taxonomy. Before molecular biology became possible, organisms were sorted by their appearance and special structural features. Unfortunately, some of those features tended to evolve independenly multiple times. A good example is the heliozoa -- sun-shaped microorganisms. Turns out the group actually was spread over three kingdoms -- chromalveolates, rhizaria and the green algae! (Nikolaev et al. 2004, PNAS)

Actually, the entire non-photosynthetic stramenopile group mostly consists of stuff that were confused with something drastically different:
- Labyrinthulids and Oomycetes -- thought to be fungi
- Blastocystis (can cause disease in humans) -- thought to be yeast (fungi) -- looks like yeast morphologically!
- Actinophryids -- a remnant of Heliozoa
- Opalinids (amphibian gut endosymbionts) -- used to be confused with ciliates
- Bicoecids -- easy to confuse with generic small things with two different flagella. The fact that there's a genus Pseudobodo might hint at something... (Bodo is a kinetoplastid in the Excavate kingdom, relative of the trypanosome with its awesome kDNA)

I'll elaborate on this at a later date... exam season is near!

Main points:
- Protista = Eukaryotes that are not Plants, Animals or Fungi
- Multicellularity arose several time independently and is therefore not a relevant trait... kelps are huge and multicellular, but are still protists (brown algae)
- Size does not matter: aside from seaweeds, there are plenty more macroscopic protists. Some unicellular ones get quite huge!

Hope this clears up a little bit of confusion...

And apologies for irregular updates... too much stuff going on at this time of the year!

Sunday Protist -- Saccinobaculus

If you're a unicellular organism, chances are you might want motility at some point or another. Being able to move helps escape predators, find food, find better sunlight access if you're photosynthetic, find a partner for some nice quick steamy sex; as well as entertaining easily-amused cell biologists.

Cell motility tends to fall into two (crudely-defined) broad categories:
1. Amoeboid -- cell extends pseudopodia ("false feet") and pulls itself into a particular direction along a surface.
2. Flagellate -- cell uses whip-like flagella to propell itself through a fluid. The flagella can be short and numerous, as in the cillia of a Paramecium, or long and few in number. You'd expect the flagellum to originate in the back of the cell, pushing it forward. Our sperm do that. However, interestingly enough, the majority of eukaryotic life voted against posterior flagella. Animals and their closest relatives, fungi, form a group called opisthokonts -- Greek for "posterior tail". Almost every other eukaryotic organism has anterior flagella -- and at least a couple of them. We're just weird.

There's also adhesive-based motility, where the cell is like a rock climber -- it anchors itself to the surface, uses cytoskeletal motors to move ahead, and then abandons the anchor. Diatoms and the malarial parasite use such technique.

However, there's something even weirder. (this is Protista -- there ALWAYS is something weirder!)

Imagine you're floating around in fluid, and you just can't be bothered to whip things around on the outside. Nor do you feel like protruding pseudopodia along a surface, like some lowly amoeba. Nor do you want to associate yourself with the brown algae because you're racist like that. Or rather, imagine that evolution does weird things. It really does...

What would you do?

This creature decided it wants to be a snake-in-a-bag:


Meet Saccinobaculus, an anaerobic resident of the gut of the wood-eating cockroach Cryptocercus. The stiking feature in the middle is the axostyle -- a think bundle of microtubules (cytoskeletal structural elements) that functions in a similar way to the muscle tissue... of a snake in a bag, which is what the name really means! This axostyle is highly motile and wriggles around inside the cell, causing it to move. This seems to be a rather inefficient mode of motility, but the creature hasn't gone extinct yet, so it can't be that bad.

But you have to see it in action:

I searched all over the internet for a movie of a Saccinobaculus moving about. Unfortunately, I failed to find any. Either my search skills suck or there just isn't any publically available out there yet. So I'll have to make do with a crappy clip I shot in class. Appologies for the shitty quality, and half-deteriorated specimen. As soon as I have legitimate access to a professional scope with a decent camera, and acceptable specimens, I'd try to fix this...

So next time you catch a harmless snake and throw it in a plastic bag, for whatever awkwardly surreal reason, be sure to remember that there's an organism that moves like that for a living. And please don't hurt the snake -- they're beautiful animals!

This advice is serious: If you have access to a microscope, and some wood-eating roaches, or Zootermopsis termites nearby, please remove the gut of one and examine it under the microscope. You'll be amazed by what you find! Unfortunately, the organisms tend to die quickly upon contact with air, so you can't really culture them for your enjoyment...

(delinquent) Sunday Protist -- Chaos

A genus that sums up my life perfectly:

Chaos (Amoebozoa)


We were looking at amoebae today. This one is quite huge -- a couple milimetres across, multinucleate and slow as an...amoeba.

Good site with background info on amoebae

(Chaos is the reason I'm falling behind on this Sunday protist thing -- midterms, research, time management issues, general loss of sanity, etc...)

And no, next entry will not be Phallus

I'm ashamed of you, California!

Having practically grown up in Bay Area (9 years of my childhood), I'm quite disappointed to hear about Prop 8, and the anti-gay marriage vote. I've always considered California as a special civilised part of the US, a shore of liberal sanity next to the shamefully fundamentalist South and Midwest.

I simply cannot comprehend: why on earth could anyone, anyone, be offended by legalised gay marriage? I mean, is anyone forcing you to have one? Does the encouplement of gays hurt anyone? Do you seriously get physical injury from seeing two girls kissing or guys holding hands? If so, perhaps you should take greater care when playing with yourselves. If your mentally-demented deity will send people to hell for it, why not let them go there? There will be more chances of you getting into your heaven of choice -- think of the gays as your competitors. If the applicant admission average is lower, more chances of you getting in. How in the hell could you have a problem with that? I can't even understand why fundies would oppose such liberties. I cannot understand how any harmless liberties could be opposed.

Including weed. Weed only makes people mellow and benign, how could that be of any harm to society? If anything, alcohol is a far more vile substance. But I guess the Christian god says booze is ok, thus we'll allow it. He said nothing about Cannabis sativa though, therefore it's bad. Also, teh paganz smoke it. Therefore it should be banned.

How much longer must we be governed by medieval laws based on the customs of a developmentally-challenged bronze age society in modern-day Israel? Why the hell should the ancient shepherds of the Middle Eastern deserts have a say in how we live our lives today?

It's not like the ancient Palestinian civilisations were worthy of any admiration, even back then. Intellectually and technologically behind their own peers, exceptionally misogynistic, racist, xenophobic to the extreme... viciosly intolerant even to their own original thinkers. I simply refuse to admire such a society -- even Rome, with all its problems, is far more pleasant. The Waorani are far more attractive -- at least they had the humility and honesty to admit they were tired of their endless bickering and spearing raids.

Needless to say, yesterday's results made me quite happy! I'm not an American, and therefore had no say, but luckily sanity won (even if barely). The Democrats will be far from perfect, and are plagued by plenty of problems ranging from the Bush's awesome legacy to their own incompetence. But at least they're not theocrats. Oh thank god for that. I would not survive a day in a theocracy, for I cannot keep my mouth shut. I suck at censoring myself... would run into so much needless trouble. Also, if I happen to be quite certain I'm right -- I am right. Until proven wrong. The fundies are right... until sufficient therapy and medication. Stalemates are boring...

Although I must admit, this feeling of beckons irresistably, akin to some mind-numbing drug. You know it's not real, you know times ahead will suck (economic crisis, etc.)... but, so tempting for your mind to shut down the skeptic faculties and enjoy the party.

Yesterday was a joyous day for many who have lived to see the day a slightly more pigmented member of our species be able to hold office. Perhaps we may live to see the day where posessing a Y chromosome is no longer a strict requirement.

Perhaps, (this is a wild fantasy) one day... we could live to see an atheist elected to office! What if there will be a time when a presidential candidate does NOT have to end every single speech with "God bless" and the likes. Perhaps, a day will come when we will no longer be America's most mistrusted and hated minority! Further yet...perhaps, someday, freedom from dogma will become a cherished goal embraced by the whole society! Perhaps a day will come for us all to embrace intellectual liberty and pursuit of happiness in truth, a day of healthy balance between skepticism and wonder. A day when the majority appreciates life as it is, living it to the fullest rather than awaiting an eternal heaven that will overwhelmingly most likely never come.

We have a long way to go. Can we?

I'm cynical. Prove me wrong, and I will gratefully succumb to euphoria. Please help me reject my null hypothesis...