Field of Science

Homage to RefWorks...

I wish Blogger had RefWorks citing capabilities... I've gotten spoiled by clicking the 'cite' button to cite stuff. Here I actually have to write out the full citations. By hand. The horror.

Luckily, I can preformat stuff there and just copy it over here. Blogging has just got a ton easier.

Sadder than my newfound dependency on citation managers is that I actually think they're like the coolest thing ever. There was actually a rush of euphoria when I discovered cursing the process of typing bibliographies is a thing of the past! I even investigated all the various citation styles and...yes, found my favourite one.

I have a favourite citation style: of the Current Opinion series. I even have a rationale for liking it. Look how neat and easy to follow it is:
Cavalier-Smith T: Predation and eukaryote cell origins: A coevolutionary perspective. The International Journal of Biochemistry & Cell Biology 2009, 41: 307-322.
The bold formatting option exists to be used, either for the author or the title. The author is usually first anyway, so it makes more sense to bold the title. The numbered in-text citations [1] make it easy to follow review papers without the clutter of full in-text references. (although the full format comes in handy at time too...) The only issue I have is the year appearing at the end. I prefer the pub year to appear right after the author, since in biology it's fairly important to know when stuff was said/done. I hate that about the wretched MLA: they don't even use year in their in-text refs!

I randomly blogged about citation styles.

I think I've just reached the epitome of geekdom. To beat that, you must argue for YOUR favourite citation style.

However, in this post is a preview of paper I will be working on translating into English for you guys, from the TC-S dialect of academese... it's on the evolution of eukaryotes from prokaryotes. Fascinating stuff!

Now I'm actually gonna do it...

Science as a journey through alien worlds

Running a gel, thus perfect time to blog. Perhaps if I write stuff in the lab, it may actually turn out to be marginally intellectual.

Hopefully my gel won't turn out to be something like this again:


I hate genotyping - the work itself requires the intelligence of a brain-dead foetal monkey, yet manages to find a stunning variety of ways to fail. And when it does work, it usually shows everything was wildtype anyway. Or maybe your mutant-specific primers failed. You should probably remember to run a positive control next time. If you have one, that is. And when it does work, you can brag about find a homozygous line amongs the seeds you ordered from the stock centre. Nature-worthy achievements right there.

Actually, most lab work is about as mundane and intellectually uninvolving. The planning and literature reading, data analysis and troubleshooting(!) can be quite exciting and tend to involve plenty of thinking, but you only do that in-between the endless repetitive pipetting and mixing chemicals and following protocols. I think research probably involves one of the biggest intellectual (and emotional, heh) rollercoasters of all professions, which is why only the very insane can handle it.

[did I run the DNA off the gel yet... no, phew.]

I do enjoy microscopy, however, which is considered by some to be repetitive and mindless as well. I cannot disagree more. It's an artistic break from the gels and protocols - you have a lot of factors to play around with to obtain the best image you can. Microscopy is also very dangerous, a wonderful way to obtain false positives! It's extremely easy to tweak the image to see what isn't there, even unintentionally. A substantial component of the art is to obtain sexy images without sacrificing the scientific validity thereof.


As children, many of us have dreamt of fantasy alien worlds, to be much disappointed upon finding out we would most likely never encounter any; not within our lifetimes anyway. However, it is wonderful to know that alien worlds are not confined to what lies beyond the Earth's atmosphere! (or present time...) They are all around us, ready to provide enchantment and fantasy to anyone who invests enough to explore.

To a mathematician, beauty may lie in quantifying forms or dynamic phenomena, or working with abstract worlds far beyond the imaginative capacity of the human mind. To a fiction writer, fantasy worlds thrive in his mind not much different from the form taken by reality itself. To an astronomer, the alien worlds are almost within reach - just barely visible, yet not ours to manipulate. For me, foreign worlds exist under the lens of a microscope, where if you magnify anything far enough, you can spend a lifetime wandering amidst the surreal landscapes unseen by naked eye. The life of or within a cell is fascinating enough conceptually, but that mysterious aspect of it being beyond our 'scale' makes it not much different from a childhood fairytale or a sci-fi novel - except that it's real!

On a more abstract level, science itself is a foreign world for exploration (along with math, the arts, etc.). Upon liberation from what Carl Sagan calls "the anaesthetic of familiarity", the mundane everyday world around us becomes full of tantilising mystery. Science is a way of unraveling some of this mystery (I'll argue, the optimal way of dealing with natural mystery), an ardurous journey through the unknown worlds. It's rather fractal-like in nature - the more you explore, the more questions arise; the deeper something is examined, the more detail beckons attention.

I think a good analogy for the scientific journey could be hiking or climbing - the act of walking along a trail is quite repetitive: all you do is place one foot before the other. After some time the scenery begins to repeat itself, and one wonders how anyone could enjoy outdoor activities at all. But many do, and probably few ever notice the monotony of walking, or climbing, or paddling a kayak... for there's always something fresh to look at, something wonderful to appreciate and enjoy. It's fairly easy to knock off the 'anaesthetic of familiarity' for an outdoor enthusiast - the escape from the chaos of the human 'world' is sufficient to make the journey worthy of the physical investments. The threat of an occasional failure, the pain of stepping on a too-unstable rock... is usually not enough to deter one from actually enjoying the exploration itself.

Science is quite similar - there is the monotony and rigorous exactness required by the scientific method, the endless protocols, the multitudes of failed and inconclusive experiments. There is the threat of losing one's job upon failure of publication - the world of 'publish or perish'. It seems one must be insane to voluntarily engage in such activity, much less enjoy it. But just like the monotony of walking is instantly forgotten upon the sight of a rare bird or an overpowering landscape, the monotony of science is instantly lifted upon the sight of a contradicted null hypothesis, or the sight of a rare species, or the ability to actually see a cellular process in action in real time... (perhaps for a chemist, the synthesis of a brand new chemical never before produced on earth could induce a similar rush or euphoria?)

But just as one does not go on a hike expecting to see a rare bird (lest the foiled expectations lead to a wrecked mood), one cannot go into science expecting to make great discoveries. The very process itself must be tolerable, and hopefully captivating enough, to keep going. Sometimes you get excited about the potential outcomes of an experiment, only to discover your results are utterly inconclusive and the story is far more complex than previously imagined. I think what makes science quite suitable for an insane type of mind is the ability to actually not mind such disappointments, and savour them as a testament to nature's superiority and infinite complexity.

After all, we may rest assured that we will never run out of work to do, just as an outdoorsman would never run out of places to explore. Now isn't that a comforting form of eternity?


[genotype results: all wildtype. Time for more PCR!]

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;">

EDIT
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!

Public apology to prokaryotes

Dear Domains Eubacteria and Archaea,

I have previously stated that while biochemically sophisticated, you're just lipid bags of biochemistry devoid of any worthy internal structure. Consequently, I've ignored you due to a personal aversion to biochemistry and the idea that your innards are too primitive to be of any interest to the cell biologist in me. I have been mislead to believe that having your DNA immediately enshrouded in fat* was a prerequisite to being a structurally interesting creature.

When browsing through Nature Reviews Microbiology, I came across a discussion of multicellularity and specialisation in some hyphal creature. For a split second, I thought "Wow, there's hyphal prokaryotes?!" and quickly smacked myself in the head thinking "Just because it's microbiology doesn't mean it's prokaryotic, you dumbfuck!" So I avoided the article in utter embarassment.

Today I've come across an explicit mention of a hyphal, multicellular prokaryote - Streptomyces. I could not believe it -- bacteria being confused with fungi, of all things?! And...wait...multicellular?

I soon found a few articles confirming its existence. Including that Nature review I scuttered away from...

Here it is:

(Source)


Source of image has a great overview too:
http://openwetware.org/wiki/Streptomyces:Other_Bits/An_Introduction_to_Streptomyces

I was wrong. I would hereby like to retract my prior statements about structural primitiveness of prokaryotes. Please forgive me!

Signed,
--Arrogant eukaryote


And meanwhile I gave all this hell to zoologists and botanists who would exclaim: "Oh protists -- the primitive eukaryotes!" Must...not...go off on a rant... Oh the hypocrisy...


*EDIT: Nevermind the lipid-wrapped DNA statement:
http://schaechter.asmblog.org/schaechter/2007/06/planctomycetes_.html
Couldn't nature leave ANYTHING for us to 'dogmatise' over?

Overcome by madness...

Once again, apologies for lack of posts -- our university is putting on an undergrad research conference this Saturday, and the slides aren't quite finished yet. Had loads of crap due today, along with a quiz in the 9.30am class I seldom attend. Also, I accidentally ventured across something interesting and tangential to my research, and had to resist the urge to dig further. Unfortunately, I lost that battle, and consequently created extra work for myself.

Anyone have any idea how to balance research with coursework life? It tends to devour your soul as you branch out akin to a plasmodial slime mould, engulfing more and more territory and stretching thin your precious cytoplasm. Eventually, you just have to retreat from side branches to generate a sense of direction... and form fruiting bodies, etc. Ok, I have no idea how that ties in with the analogy...


Running on 4h of sleep implies an excuse to lazily post a link instead of real blog content. Here's a Tree of Life page on dinos... enjoy! It has pretty pictures!

Back to madness...