Field of Science

Excerpts of an old 'lab notebook'

I got my first microscope for my 9th birthday. Soon afterwards, I discovered pond water, and the true character of scum. I found exactly how to satisfy in me the innate thirst for alien worlds we all share. All one needed was a change of scale. I also happened to be quite obsessed with insects at the time...

I recorded everything, especially since I didn't have a camera and wanted to remember everything I saw. This introduced me to the scientific method. Naturally, being a naïve 9-year-old, you think you're making some earth-shattering discoveries and painstakingly record and cherish your data. Looking back, it's rather primitive... but still, I remember being proud of some of those drawings!

In a way, those were the golden years when most of my intellectual progress happened. Afterwards it all kinda goes bleh, and real life tries its damn hardest to knock all the creativity out of you. Wish I'd done much more then...

I took the photos in a hurry since the notebook is at my parents' house... excuse the crappy quality, and try to enjoy! Oh man, what a nerd...






I may redo this post once I get better pictures...

Writing drought lifted...

Apologies for disappearing for a while. Some incidents in my personal life have interfered with my writing. Should be back in the mood again, and hopefully can finally get the protist stuff on the road... until the next roadblock anyway.

Oh, and guess who gets to see James Randi on Monday! =P

Start-of-term shitstorm

Sorry, guys... behind on my Eukaryote Biodiversity posting... got caught up in a LOT of madness related to 6 courses and some very horribly neglected research. Tonight would've been great, had I not been subject to diethyl ether vapours for about 3h in o-chem lab, thereby making me veryyyyy sleeeeeeepy...

Daniel Dennett came to speak at our university last night. His talk was great (on memetics and 'Darwin's Strange Inversion of Reasoning')... needs a discussion post as well, but not on a mind full of ether. Apparently this is gonna happen in every o-chem lab, so once a week.

Actually the ether effects are subsiding, but I'm still lazy and tired. And I have a review paper to read for tomorrow morning. I'm on page 2...

Towards the middle of the term I tend to adopt a progressively more liberal attendance policy (skip class), so this shitstorm should subside into a brief calm soon...

Happy New Year!

Happy New Year and best wishes for 2009, everyone!

Vancouver is thoroughly covered in snow! As a former resident of Toronto, I get plenty of entertainment watching the locals become completely stumped by pieces of frozen water. Not that the Torontonians deal with it much better -- counting down the days until winter ends is no way to consider yourself adapted to the climate -- but at least they've invented the plough by now, which sets them approximately 9000 years ahead of Vancouver.

It's quite beautiful and nearly surreal, the marriage of the mountaneous and maritime great Northwest with the undeniable purity and beauty of proper (snowy) winter. If only we could get some frost here; say, -15 or -20. That'd be nice. Mwahaha.

I hope to get some pictures tomorrow, to share the enjoyment. If it doesn't all turn to slush by then -- the inevitable and fast-approaching fate of Vancouver snow. It makes me quite sad... for often the snow has barely lived a day before it must turn to mush, and end its ephemeral existence so ungracefully. Sometimes the snow is born from the skies an ungraceful slush, and clings to your every footstep, begging to be accepted as the real thing. But you trudge on through the muck, stepping on the pleading slushiness of the bastard child of rain and snow -- a mere hybrid, not to be accepted as one or the other. And then you get wet. Thus killing the whole poetic-ish mood of the scene, as I have here.

I had some plans for 2009 blogging -- namely the celebration of evolution and biodiveristy by going through each of the phyla on the Keeling et al. 2005 tree. That's rather ambitious, I must admit; and I'm rather lazy and undisciplined. So we'll see how that goes. Hopefully not as bad as trekking along Vancouver's sidewalks these days. Seriously...

Vacation

Going to be mostly absent from the internet until the 4th. Happy holidays, everyone!

Probably won't be able to post protists until then, but expect more, much more, in the new year. We are celebrating evolution in 2009, after all!

Apologies for vanishing for the last two weeks -- finals can do that to you! (I think I survived...)

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:


Source

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:


(source)

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)

source

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