Eukaryote Biodiversity Series 01: Looking at Life

(Just pretend I posted this on Thursday, ok? Thanks! <_<)

Protista is a vast kingdom surrounding the three miniscule enclaves of Fungi, Animalia and Plantae. Together, they form the domain Eukarya, a humble accident on the shores of vastly prokaryotic life. In the Eukarya, Protista is the most diverse and fascinating place: a realm seldom touched by human exploration; a realm with many secrets beckoning our attention; a realm of strange mystery and eerie familiarity.

To celebrate Darwin Year, evolution and biodiversity, join me on a journey along this land -- so we can wander lost together!


(Hopefully) Resolving some confusion
I've touched on this before, but since this is an introductory post: There is some confusion with respect to what Protista includes, and doesn't include. This confusion permeates the majority of reputable government and educational publications by non-specialists. For example, the government of Nova Scotia thinks: (emphasis mine)

The kingdom Protista is used to group most single-celled organisms, except bacteria and blue-green algae. Protista is a large and variable group containing both plant and animal characteristics. This group includes about 50,000 species of protozoans (first animals) and between 8,000 and 12,000 species of algae (simple plants).

Protists are mostly microscopic and have no organs or tissues. They are single-celled but may occur in colonies. They may be free-living on land or in water, or live in association with other plants and animals. Locomotion is achieved by waving tiny hair-like threads.

1. Blue-green algae are bacteria. Also, Protista does not include myxosporidia (animals) and yeasts (fungi).

2. Most protozoans have absolutely nothing to do with animals. They are fundamentally different lineage. Same with the algae. More importantly, no modern organism (alive today) is a first anything. Fish are not our ancestors. Our ancestors likely looked fish-like at some stage. Modern fish are a distinct lineage with their own long and ardurous evolutionary journey. It makes as much sense to say modern fish are early man as it is to say modern man is early fish...

3. Kelps can grow up to 60m. They have distinct tissue types -- a holdfast (root), stipe (stem), and blades (leaves). Red and green algae are multicellular as well, with distinct tissue types. Multicellularity is more common that one would think, and has occurred at least 8 times independently even if you take a conservative approach.

4. Amoebae, Toxoplasma, diatoms and Saccinobaculus disagree.


But don't take this as an attack on whoever painstakingly put that page together. As you see, Protista is a rather diverse and poorly-unified kingdom. Part of the reason is the 'racist' arrogance of the residents of one of the isolated enclaves -- Animalia. Fungi, Animals, Nucleariids, Ichthyosporeans and Choanoflagellates could coexist peacefully in Kingdom Opisthokonta, unified by proudly wearing a tail on their asses, instead of waving it before them like all normal Eukaryotes. Unfortunately, some clans of the Animal tribe can barely accept sharing an association with fellow Animals, let alone little moldy unicellular things that give us beer. Instead, we prefer to spend our lives entangled in a taxonomical nightmare.


Brief History of Protistology
The main reason for the taxonomical mess is historical. Before the 1600's, there was no way to see microscopic organisms, so no one had a reason to suspect their existence. Life was sorted into plants (green, static) and animals (motile). This may even be an innate categorisation! Fungi were categorised as plants, for they didn't seem to move. Signs of microbial presence were just seen as rot, which was a manifestation of 'foulness', etc.

Then came the 17th century with Robert Hooke and Antonie van Leeuwenhoek, who created the first microscope and discovered the first unicellular organism, respectively. Hooke looked at a section through cork and discovered cells, apparently named for their resemblence of the monastic ones, or so says Wikipedia:


(Hooke 1665 Micrographia)

Leeuwenhoek was a Dutch cloth merchant who had never gone to university, thereby retaining some creativity and intelligence. He invented a special technique for making microscope lenses which was later found to involve melting glass into spheres, as opposed to grinding it. In fact, we got to try out the technique in class once. Never thought a protistology lab could involve propane torches and glass melting. The scope mimics something like Leeuwenhoek's:



but simpler, of course. Amazingly enough, it actually works! It's quite astonishing that you can actually see microorganisms in pond water through that thing! Microbiology was no longer some distant world kept apart from us by rediculously expensive and complicated optical instruments. A glass sphere is enough to observe it! (we had to make one of those for a lab exam afterwards -- this guy managed to involve a propane torch in a freaking protistology lab exam, somehow...truly memorable!)

So using such a simple tool, Leeuwenhoek discovered the first unicellular organism, likely some sort of ciliate. Apparently there aren't any drawings of it out there; if anyone knows whether Leeuwenhoek ever made a drawing, could you let me know where to find one? I'm utterly curious! He does have some bacteria though:



Afterwards, there was an explosion of people playing with scopes and painstakingly recording their findings. Some examples from Haeckel here and more scans here.

Now life no longer made much sense. Of course there were still things that looked like plants (sessile algae, eg. spirulina) and things that looked like animals (eg. ciliates) -- those were called protozoa, since they were considered to be ancestors of animals (most aren't, as we shall see later). There were some hyphal non-green forms, but those were fungi... which were considered to be plants for a long time. Mycology is still often considered part of botany, and is done in botany departments to this very day.

Over time, people got more and more confused as discoveries piled up. You had motile algae, which didn't quite fit the 'plant' category very well. Fungi also resisted the plant kingdom as more and more was learned of them. Eventually, fungi gained independence. Protists were classified into 'algae' (Plantae), 'protozoa' (Animalia), 'sporozoa' (Fungi). Since those organisms shared a lot in common, at first glance, they were granted their own kingdom in 1866 by Haeckel -- he named the them Protista.

A more recent rendition of this idea:


(source)

This thing honestly makes my eyes hurt. There's just so much WRONG with that tree I barely know where to start. I mean, back in 1969 when this was made, molecular biology was barely starting so they didn't know any better. The tree was constructed mostly on morphological data, which can be extremely elusive due to evolutionary convergence. I'll discuss that in more detail later: there are some wonderful examples of this. The entire non-photosynthetic heterokont group had to be assembled from bit and pieces all over the tree once molecular data came out!

Another, more fundamental, issue with this tree... is this stupid notion of some forms of life being 'beyond' others, more 'complex', more 'advanced', more 'evolved'... this idea that evolution pursues progress, and we're at its apex. Evolutionary Creationism, nothing less. "Fine, if there's no loving god... then there must be loving evolution that worked 3.8 billion years to create us in the end!"

(moreover, in terms of 'evolvedness', we lag far behind the bacteria, due to our retardedly long generation spans...)

You'd laugh, but some professionals hold this kind of view, without realising it. Oh how many times I've mentioned my interest in protists, only to be subject to "Protists? Oh, the primitive eukaryotes!" I'm talking about professors here. I argue they're not actually all that 'primitive', that term is fundamentally flawed in this application. They look at me funny and avoid the topic altogether...!

Moving on, after many long arduous years of poor grad students (and undergrads! =P) slaving away at the bench, thus far we have something like this:

(

(Taken from here; originally from The Tree of Life: An Overview. S. L. Baldauf, D. Bhattacharya, J. Cockrill, P. Hugenholtz, J. Pawlowski, A. G. B. Simpson. Chapter 4 in Assembling the Tree of Life (Eds. Cracraft and Donoghue, Oxford University Press, 2004)

There is still much uncertainty about the root of eukaryotes; that's a topic for a later post.

Along the way, there was an interesting hypothesis based on some organisms appearing to lack mitochondria. It has been disproven upon further investigation, but modern textbooks still parade it around as fact... almost a whole decade out of date! More on that later...

Hopefully now we may have a clearer idea of what a protist is, as well as a bit of history of the field. Over the course of the year, I'd like to journey around the Keeling 2005 tree and also discuss some themes like multicellularity, endosymbiosis and the dangers of morphology. I hope to share some of the wonders of this alien kingdom as I just begin to explore it myself. Carl Sagan dreamed of alien life beyond -- I believe I've found his aliens. All he had to do was look closer here on the Pale Blue Dot!


Some resources:
The smallest page on the web - basic intro stuff, nice pictures
Tree of Life - put together by experts in various fields

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

On the 7th day of creation...

...god took a few hits of LSD and created Protista.


This solves the great mystery of why the Bible neglects microorganisms... the ancient priests realised the dangers of letting imagination run wild and tried supress hallucinogens as much as they could. Lest you get another protist-ful of madness out there!

Some evidence supporting my hypothesis statement of profound enlightenment:

1. Kinetoplasts

Srsly, WTF?

You know how normal people pack their genomes into a few chromosomes in a nucleus, and then transcribe and translate at will?
Said normal people also have little anucleate bacterial friends within them, mitochondria, who stored away most of their genes in the host nucleus, and kept a few for themselves. They have circular DNA, which is then transcribed and translated like a normal bacterial genome, more or less.


Well, these things decided that was simply too boring for them.

Instead, let's string about 5000 varieties of circles together with a couple dozen large circles thrown in for extra fun. And by 'string together' we mean: make chainmail.

What an epic idea! DNA chainmail! Can you imagine how much hallucinogenic chemistry you'd have to experiment with to generate such ideas?

And then we're gonna pack this chainmail into a very tight disk, and shove it right below a flagellum, in a mitochondrion. And yeah, rotate it during replication...


Crithidia fasciculata
(http://www.biochemsoctrans.org/bst/033/1409/bst0331409f01.htm)
The arrow points to one of the few dozen large circles.

('normal' mitochondrial DNA:

The circular string in the sea of junk (suspension medium)
www.bios.niu.edu/core/)


But those are no ordinary circles of DNA.

They are required in order for the mRNA transcript from the gene on the large circle to code for the right protein. If you sequence the large circle genome, you'll find lots of gibberish and very little gene-like content. Those 5000 tiny circles are involved in a process of editing this mRNA transcript to code for something marginally sensible. In fact, the resulting proteins correspond quite well to their conterparts in the saner organisms...

Expect more details on this sometime eventually later... (when I learn some more about it myself)


2. Algal vision
And this thing:


(Photo: Haruyoshi Takayama)

The spherical thing there is an ocelloid. Basically, camera eye entirely out of subcellular components: lens and retina. It can likely form an image on said retina. Great -- but Erythropsidinium is brainless! What does it do with the image? Why does it bother?

There's quite a few other examples of algal vision, although I think the ocelloid is the most elaborate seen so far.


3. Cortical inheritance (Paramecium)
(Beisson & Sonneborn (1965) Cytoplasmic inheritance of the organization of the cell cortex in Paramecium aurelia. PNAS 53:275-282)



Take a row of cilia in Paramecium, revert it so it points backwards... and watch them divide -- copying the backwards row of cilia into the next generations! In no way was the genome altered in this process -- likely during cell division the original cell is used a bit like a template, thereby prompting this weird phenomenon of epigenetic inheritance...somehow. To my knowledge, precisely how this works is yet to be understood, still... over 4 decades later.

---

The creator had some good LSD or crack or shrooms or whatever... if only he/she/it could share some with us... sigh.

Actually, it did. Evolution gave us coca, Psilocybe, Cannabis, Ayahuasca, opium, Tobaccum... a perhaps a vast unexplored realm of even more drugs out there awaiting discovery!

(One wonders if smoking a certain protist could yield similar effects... )

Woes of broken internet

Had spotty internet connection at home for the past week or so. That was compounded by the usual midterm madness at school, thereby resulting in slight neglect of certain blogging duties. Appologies... I really shouldn't do that!


So to redeem myself a little... ciliate diversity! Pretty and quite trippy:


(Finlay and Esteban: http://members.magnet.at/p.eigner/Diversity.html)

Why are chromalveolates so damn sexy?

Sunday Protist -- Trichonympha

(http://www.microscopy-uk.org.uk/mag/artmar03/rhtermite.html)

Trichonympha

Termite gut symbiont, 200-300 microns long (huge for a protist). On the inside, bottom half, are pieces of wood -- termite gut protists digest cellulose for the termite, who feeds on the metabolic byproducts. The round thing in the centre is the nucleus (with permanently condensed chromosomes), and rows upon rows of flagella. Being a parabasalian, this creature lacks mitochondria like ours -- instead, they have been reduced to hydrogenosomes, which produce hydrogen gas.

The termite gut is a lush ecosystem FULL of cool things, more of which will be posted later. You also have episymbiotic bacteria covering some of the symbiotic protists, resulting in an ecosystem-inside-an-ecosystem type of environment.

Hard to resist the compelling urge to start slicing open random insect guts in hopes of finding protists...

Sunday Protist -- Diatom

When UV light bounces off chlorophyll, the frequency is shifted towards red (fluorescence), which can be safely picked up and observed through a UV filter. What is awesome about UV work is that you can view it simultaneously with our own spectrum, since we don't notice when UV light is filtered away. You can't do the same with substances whose excitation frequencies (the incoming colour that later changes) lie within our visible spectrum, since you have to filter out a band of colour - making the filtration pretty obvious. Thus, you can't simultaneously view GFP (green fluorescent protein) and normal light, since you'll have to filter out everything but green, which is the emission frequency (the resulting colour).

Fluorescent microscopy is a powerful tool in cell biology, as it enables one to "colour" certain proteins, and find them via fluorescence. You can do live cell imaging with that, and observe real cellular processes in vivo, as well as creating time-lapse (movies) and stacks (3-D reconstructions).

I wish people were taught about real cells in school, as opposed to that hideous textbook thing (which does NOT exist -- there is no 'typical' cell!) Cells are so alive and dynamic and exciting...all that gets thoroughly lost in those cartoon diagrams. Can't we provide highschool educators with our sexy movies of real cellular phenomena in action? Should be cheaper than textbooks themselves! And much more informative, not to mention memorable!


Now back to our diatom. Since UV light is converted to red upon hitting chlorophyll, what does the image stack tell us? Well, you can see certain compartments emit this red light, indicating the presence of chlorophyll. You may or may not have heard that diatoms are phytoplankton, meaning plant-like plankton. They are actually not particularly close to plants at all -- diatoms are brown algae, the ancestor of which has engulfed a green alga at one point, and incorporated it as an organelle. As a result, the chloroplasts in diatoms have two extra membranes around them, coming from the original green algal host. This is called secondary endosymbiosis -- a host engulfed a host of a cyanobacterial descendant (chloroplast)!

There's also tertiary endosymbiosis -- a host engulfing and host of a host of a chloroplast. Some of things have an extreme number of membranes layering each chloroplast.

I'll discuss endosymbiosis in more detail at a later day, but back to our diatom. I'm a bit dense, so it took me a while to remember that diatoms are phytoplankton, for they don't particularly look like plants or green algae -- they're not particularly vibrantly green like the green algae. But playing around with our UV lamp after a whole day of DAPI imaging (to see nuclei in plant cells), I threw on some seawater samples on the slide, and got views like the following:





And that little thing with a tail near the top may be a dinoflagellate of some sort, perhaps. Catching those things with a camera is nearly impossible...they like to move!

Anyway...most diatoms you find tend to be empty shells, as opposed to the live organism itself. So you often forget that they are in fact photosynthetic. I think the autofluorescence drives that point home quite well. Now we remember. Also, you could possibly identify plastids based on their autofluorescence emission, but I'm not sure how it's done yet... that would be topic for another day.

Another cool thing about diatoms -- when they divide asexually, the top shell separates and forms a bottom, which is smaller than the top. The bottom shell becomes...the top, and forms and even smaller bottom. Consequently, several generations later you end with a population of very tiny diatoms, so they have to somehow get bigger again. So they enter the sexual cycle, fuse and dissolve their old shells entirely, forming a new, large, pair upon separation. That's why you find a gradient of sizes within the same species.

Happy diatom worship!

And then it suddenly... EXPLODED!

An image sequence of a cilliate I got today, while taking optical sections:








(40x, Namarski phase contrast)

The heat from the light source must've got to the poor guy... =(

Sunday Protist - Labyrinthulomycota

Cute little marine protozoans that run around through 'tunnels' of their ectoplasmic net. Featured above are Aplanochytrids, which glide along the ectoplasmic net without being enrobed in one. (Leander at al. 2004 Eur. J. Prot.)


(http://www.botany.uga.edu/zoosporicfungi/labyimages.htm)

On the other hand, labyrinthulids (above) travel right through the ectoplasm they secrete. They form those elaborate nets they crawl around and use to catch floating debris/prey.

Sunday Protist - Tetrahymena thermophila

(Definitely not totally ripped off of Pharyngula's "Friday Cephalopod")

Since [putative] readers of this blog are unlikely to be in church on Sundays, we shall celebrate by looking at cool little organisms instead. Worshipping protists is so much more rewarding!


(from Wikipedia)
( Robinson R (2006) Ciliate Genome Sequence Reveals Unique Features of a Model Eukaryote. PLoS Biol 4(9): e304 doi:10.1371/journal.pbio.0040304 )

Tetrahymena thermophila (fluorescently tagged, of course).

It's an aquatic cilliate -- a microscopic organism covered in little hairs (cilia) it uses for swimming.

Those creatures have two types of nuclei -- the micronucleus which is the germline, and the macronucleus which is used during the organism's everyday life (ie. somatically expressed). Upon conjugation, the old macronucleus is destroyed and the micronucleus is doubled, with one of them being modified into a macronucleus. The macronucleus genome is then duplicated multiple times -- up to 45 copies -- and the non-coding DNA is spliced off. (http://www.ciliate.org/genetics.shtml)

What a brilliant strategy: keep a copy of your genome safe and unmolested by transcription enzymes (in order to actually use it to make proteins), and have another copy amplified and optimised for everyday use.

Image you had your favourite film on a VHS tape (those ancient casette things, in case a reminder is needed!). Every time you play the tape, you damage it little-by-little, eventually ending up with loads of scratches and poor sound quality. Now you need to copy the film for a friend. The scratches will still be there when you copy it, since that particular data is permanently lost. You friend watches it few times, and the next copy is even more damaged. And so on.

So that the data is not completely lost, you can build some mechanism that edits and fixes the tape each time you play it. It notices the minute scratches, and patches those holes in the data while it can still guess what must be there. This mechanism would be fairly expensive, difficult to set up, and prone to malfunctions. This is what we animals do. Also, we have millions of cells, most of them not in the germline (ie. will not be passed on to the next generation). Mutations in those cells are usually benign and don't matter in the long run (even cancer itself is not transmitted to the next generation; although susceptability to it may be). We try to protect our germline DNA to the best of our ability, albeit in a very unnecessarily complicated, inefficient way.

The poor little Tetrahymena doesn't have a place for germline cells to be stored. Everything must be enclosed in one cell. And it's a bit too small to experiment with low efficiency complex strategies. Every joule of energy counts in its life.

When you first get your film, you could also make a copy of it right there, lock it away in a cupboard somewhere and use the other at your discretion. Hell, you can even keep it out of the box if you'd like -- if you damage it too much, you can always make a copy of the one in the cupboard. If a friend comes to you and asks for a copy of the film, you just make them a copy of the cupboard one, so the damages you've inflicted on your viewing copy do not propogate any further. Your friend also makes a viewing copy and a storage copy.

That's exactly what the Tetrahymena does. It leaves a copy of its genome for storage, locking it away in the micronucleus. The other copy is optimised for reading and is later destroyed upon conjugation.

In a way, that's kind of what we do, albeit in a rather complicated manner. Once the zygote is conceived, the male's somatic cells can all but disappear. We don't care if he dies. Oh, and after gestation and childrearing, the female can die too. Your gonads are micronuclei; the rest of your body consists of macronuclei.

Yet another example of convergent evolution between multicellular and subcellular structures?


Tetrahymena has more cool features, but I'll leave them for later. Since Tetrahymena is a convenient model organism, I'll probably return to it quite a few times.

-----------
RETRACTION(18.08.2009): The tangent about the 'adaptive advantages' of nuclear dimorphism is fundamentally flawed and therefore retracted. The reasoning is backwards, and ciliate nuclear dimorphism is in fact a testament to the generation of complexity by neutral forces. The micronucleus is almost completely packed with transposons and other toxic DNA that must be excised for proper nuclear function. Most other life simply takes better 'care' of their genomes...