Field of Science

Delicious squashed cockroach guts

Done finals for the term. Have more in June, so it doesn't seem like the end really...

And a certain Dictyopteran-endosymbiont-obsessed faculty in our department is indirectly responsible for the following 'study break':

I'm sitting there, cramming biochem, getting some studying done. Along comes a cockroach (I've spotted at least three species of cockroaches in our building already). I instinctively catch it and key it out, to subsequently determine it's phylogenetic position without the cockroaches. It was Supella longipalpa, sadly not a basal roach, and thus unlikely to host the Parabasalian zoo I was looking for (eg. Trichonympha). Further literature searches revealed only bacterial gut flora, and parasitoid wasp larvae. However, anything trumps biochem, so I decided to go have a look.

As expected, not much excitement in the way of gut flora. A couple flagellated-seeming tiny things (a couple microns) -- possibly bacteria, possibly some obscure excavate -- couldn't quite tell. Couldn't take pictures of those as our camera is too slow even for us plant people. But then I discovered the awesome that is insect tissue under polarised light:

Microscopy is truly the closest thing we got to exploring foreign universes...

Surreal landscapes...

This one reminds me of Southern Ontario fields in the winter:

(you can see why cockroaches are in order Dictyoptera - net-wing.

More Martian tripiness:

And can anybody tell me what those greenish round things are?

I really need to read up on insect anatomy... have no idea what I'm looking at most of the time. Not to mention that it's all squashed to begin with...

Sadly, as expected, no cool Parabasalian freaks found in Supella longipalpa hindgut this time. K, next cockroach!

If anyone's got some spare Cryptocercus lying about, feel free to send 'er over! My current clip of Saccinobaculus sucks arse, and that organism is way too cool for sucky videos.

Ciliate developmentally-regulated genome rearrangements

Here's the essay I did for my protistology course this term, on ciliate nuclear dimorphism and developmentally-regulated genome rearrangements (epigenetic regulation of new macronucleus formation by the old one). If you'd like to read about some weird genomes (and overall weird organisms), this might be a good start (I've referenced plenty of further reading). It's not perfect; as a matter of fact, not even near publication quality, since this was just for a class. So if something fails to make sense scientifically, please let me know.

I do intend to discuss/rewrite this here in normal English someday... just not during finals!

Now I've just spent the last hour trying to post this. Tried Pdf, but Google Docs doesn't allow public Pdf publishing yet. Tried to upload as a .doc file, but exceeded the 500Kb limit (WTF!) In desparation, I printscreened the Pdf and composed pages out of images using my good friend ImageJ, and put into a letter-sized Powerpoint. Guess what... Google Docs won't let me change the slide format so the whole damn thing is stretched!

Publishing an essay turns out to be too sophisticated for Blogger. So here we go, to everyone's greatest annoyance... I'm gonna post images. Page by page.

It's that time of the term...

Protistology final Thu, then a genetics exam 8.30am SATURDAY freaking morning, and two more exams Mon and Wed. Thu shall be dedicated to taking care of a massive hangover. On top of that, I have a shitload of lab stuff to do, because I'm so great at timing things so that everything matures exactly when it really shouldn't.

And Firefox is telling me protistology is not a word. ISOP needs to lobby some dictionaries...

I did go on a microforay, however. Don't have time to process all the images, but found a few cool cysts (I think):

The latter may be a dino cyst; anyone know?

And a girdle view of a good ol' diatom:

Off to cram study intelligently with a long term goal of retaining learned info past the final (yeah right.)

Reddit > Fark; and a note on prescriptive grammar

Had a brief argument with my friend last night about whether Fark or Reddit is better, and what do you know... this morning, Language Log happens to prove my point:

Geoffrey Pullum's article about The Elements of Style, like any other piece of prescriptive grammar advice, being a wad of fail.

Fark's response according to Pullum (original thread of fail)

Reddit's response

tl;dr -- only losers read Fark.
Besides, what the fark (<_<) style="font-weight: bold;">

Since people asked, here's a bit on why linguists tend to hate/ignore/get rather irritated by writers of prescriptive grammatical advice. Since I seem to write better comments at 5am than blog posts at high noon, for whatever reason, I'll just repost my comment here.

Prescriptive grammar has several issues:
a) to linguists it tends to be of little interests as it does not reflect the innate tendencies of language speakers, which is what the study of language mainly focuses on. Prescriptive grammar is largely ceremonial.
b) English has a particularly bad case of prescriptive grammar being based on the grammar of some [mildly] distant language, eg. Latin. Take, for example, the law against split infinitives. The only reason it exists is that in Latin, it is impossible to ever split one due to it being comprised of a single morpheme. No reason to be so against it in English! Often, it's less awkward to simply ignore such relics of the medieval days of Latin scholarship.

Prescriptive grammar (and to some extent, prescriptive style) isn't particularly productive in helping people write better. Even linguistics background can get in the way sometimes -- I've encountered several linguists who...erm, don't quite put it into practice very well <_< style="font-style: italic;">The Language Instinct. (Great book, btw, highly recommend reading it!)

Prescriptive grammar does play a fairly important role, however: it prevents languages from dissipating into thousands of tiny dialects by setting up an arbitrary standard dialect one must aspire to. Otherwise, linguistic speciation likes to happen at an astounding rate, and 'in nature', languages tend to be rather small and ephemeral entities. They are very much like bacteria, in fact! Loanwords (plasmids, if you will) are exchanged on a regular basis; even grammatical structures can be borrowed from the neighbour (LGT, if you will?).

And they can 'conjugate' too, and create offspring via creolisation -- a fascinating phenomenon where multiple unrelated languages are mixed into what is called a pidgin, and the children growing up listening to this artificial language modify it to conform to natural linguistic laws -- regular grammar, complex sentence structure, etc. I don't even think there is a strong equivalent to that among biological organisms!

I've been studying...

Thought you guys needed proof:

And then we ditched our beer cans on an unsuspecting lab's drink shelf (that's what it's really for, right? The fine art of beer arrangement?) Mwahaha, who'd like to be the next victim?

(PI's name blurred out since I doubt they'd like to be associated with the likes of us... <_< )

No really,

That's about a third of the organisms we need to know for tomorrow's exam. Their life stages/cell structure/special features too. Ignore the arrangement of non-photosynthetic heterokont phyla -- they're randomly placed. Also, I insist on calling the Cryptomonad/Haptophyte clade 'Crhaptophytes' even though it got rejected. Actual protistologists, please assist this noble cause by using that wonderful taxonomic term proliferously! Thanks.

To cite aforementioned phylogenetic mess, please use (Wavefunction, P. 2009,
SkepticWonder). Methods consist of: Chalk, modest volume of EtOH, exam panic. References: More people who would not like to be associated with the likes of us XP

Hmmm... I haven't stated anything utterly controversial on this blog yet. Here we go:

"Cell biologists are superior to molecular phylogeneticists."

(Cue 'real' botanists: "Arabidopsis is NOT a plant!!!1!!one!!!")

Let the wars begin! *cracks open another can of beer and sits down to watch*
*evil laughter*

Ok I'll stop embarassing myself with pointless rambling... I overstudied. TOKOPHRYA!!! BLEPHARISMA! TETRASELMIS! CHILOMASTIX! ACHLYA! VAUCHERIA! NOCTILUCA! CRICOSPHAERA! EIMERIA! CYANOPHORA! ...can't stop...feel bad about ignoring groups... aaaaahhhh.... (we didn't have time to cover Rhizarians though *weeps* )

J Endless Excuses, v1(1):1

My blogging style apparently asks for a new category label: "Excuses". How long before this becomes the largest category, overtaking the "Protists"?

Just spent a week writing a research paper for my protistology course... for some inexplicable insane reason, epigenetics of new MAC formation in ciliates seemed like a wonderful idea at the time. I knew absolutely nothing about epigenetics, other than that histones and miRNAs were involved. And for those who don't know, epigenetics, histone modification, miRNA pathways... are chaos of unimaginable magnitude. The sheer complexity of it all is overwhelming, as well as how much is still unknown. Non-coding RNAs are a relatively recent major discovery (early 90's, I believe), and the field has been growing at an incredible rate. And of course, there was no better way to introduce the stuff to myself than via ciliates, possibly the strangest eukaryotes on earth. It's kinda like going to a foreign country to study quantum physics in a language you know nothing about.

Then I spent a whole two nights pondering about the evolution of nuclear dimorphism, and wrote a couple pages of 'conjecture' (ie. pulling shit out of one's ass in a scientific manner). I was considering editing the essay and posting stuff here (in a less condensed manner)... anyone care about ciliate epigenetics here?

Anyway, with exams around the corner, I don't know how much I can redeem myself. There's about five exams patiently waiting to devour my brains and my non-existant soul...

I'll just cuddle up with Denial and watch a few anime series instead. Denial is so warm and fuzzy and comfy! =D

NO, BACK OFF, DENIAL... I told you we can't continue our relationship any longer! I've started seeing others... I only come to you when I'm troubled... we shouldn't be together anymore! <_<

Now that we've established that the author has imaginary conversations with an abstract noun, have a good weekend!